bluuebunny/crossref_metadata_2025 huggingface dataset:
Immediately sequential bilateral cataract surgery: an academic teaching center's experience
Authors: Qi Susan Ruyu , Arsenault Roxanne , Hébert Mélanie , You Eunice , Légaré Marie Eve , Arshinoff Steve A. , Mercier Mathieu
Published: July 2021

Purpose:

To evaluate the safety and outcomes of immediately sequential bilateral cataract surgery (ISBCS) at a Canadian academic teaching center.

Setting:

Tertiary university teaching hospital of Laval University, Quebec City, Canada.

Design:

Retrospective cohort study.

Methods:

2003 consecutive patients (4006 eyes) who underwent ISBCS under topical anesthesia from January 2019 to December 2019 were included. All charts were retrospectively reviewed. Outcome measures included intraoperative and postoperative complications, postoperative uncorrected distance (UCVA) and pinhole (PHVA) visual acuities, and autorefraction measurements.

Results:

4006 eyes from 1218 (60.8%) female and 785 (39.2%) male patients with a mean age of 74 ± 8 years had a mean preoperative visual acuity of 0.503 logMAR (Snellen 20/63). The mean axial length was 23.53 ± 1.37 mm. Most eyes had monofocal intraocular lenses (IOLs) implanted (n = 3738, 93.3%) followed by toric (n = 226, 5.6%), multifocal (n = 25, 0.6%), and multifocal toric (n = 17, 0.4%) IOLs. Intraoperative complications included 14 (0.3%) posterior capsule ruptures with 5 (0.1%) requiring sulcus IOL placement, and 7 (0.2%) partial zonulysis, with 3 requiring capsular tension rings (0.07%). There were no cases of endophthalmitis or toxic anterior segment syndrome. Mean 5-week postoperative UCVA was 0.223 (Snellen 20/33), PHVA was 0.153 (Snellen 20/28) with a mean spherical equivalent of −0.21 diopters.

Conclusions:

ISBCS performed following International Society of Bilateral Cataract Surgeons recommended guidelines is a safe procedure. This cohort of 4006 eyes had very few complications, with none attributable to the surgery being done bilaterally. The UCVA, PHVA, and refractive outcomes were good.
Is There a Role for Intraoperative Navigation During Cochlear Implantation in Patients With Aural Atresia?
Authors: Wong Kevin , Kaul Vivian F. , Fan Caleb J. , Schwam Zachary G. , Cosetti Maura K.
Published: July 2021

Objective:

Concurrent bilateral congenital aural atresia (CAA) and profound sensorineural hearing loss are rare. While not a contraindication, temporal bone and cochleovestibular abnormalities are an important consideration for cochlear implantation (CI) candidacy. Intraoperative image-guided surgical navigation may play a role during CI surgery in patients with complex anatomy, such as CAA.

Patient:

One patient with bilateral CAA, cochlear dysplasia, speech delay, and profound sensorineural hearing loss underwent candidacy evaluation for cochlear implantation.

Interventions:

Cochlear implantation using intraoperative image-guided navigation.

Main Outcome Measures:

(1) Registration accuracy, (2) surgical outcomes, (3) audiometry.

Results:

A four-year-old girl with complete bilateral CAA and profound sensorineural hearing loss successfully underwent a right transmastoid approach for CI using intraoperative image-guided navigation with sticker fiducials. Bony landmarks included the mastoid tip, tympanomastoid suture line, helical root, zygomatic root, and lateral brow. A registration accuracy of 0.9 mm was achieved. There were no intraoperative or immediate postoperative complications. Postoperatively, Neural Response Imaging was confirmed on 9 electrodes and behavioral testing demonstrated Ling-6 access at 30 dB. On most recent follow-up, she has demonstrated gains in language development, vocalizations, and uses total communication in a hearing-impaired educational environment.

Conclusions:

Children with CAA and profound sensorineural hearing loss may be candidates for cochlear implantation, with successful outcomes in the setting of complex anatomy. Surgical navigation may play a role corroborating intraoperative landmarks.
Remission of Mucosal Melanoma of the Middle Ear and Petrous Temporal Bone and Reversal of Cranial Nerve Paresis Following Radiation and Single Agent Nivolumab: Clinical Capsule and Review of the Literature
Authors: Carlson Kevin J. , Volsky Peter G.
Published: July 2021

Objective:

We report disease remission and recovery of fifth and seventh nerve paresis in a case of primary mucosal melanoma of the middle ear and petrous temporal bone.

Patient:

A 74-year-old man developed sudden, profound, right sided sensorineural hearing loss, disequilibrium, otalgia, and cranial nerve V and VII dysfunction. Imaging demonstrated an unresectable, osteolytic lesion involving the middle ear and anterior petrous apex. Melanoma was diagnosed via in-office biopsy; whole-body metabolic imaging revealed no other primary site.

Intervention:

Multidisciplinary management included radiation therapy (30 Gy, 10 fractions) followed by induction (five cycles, q2w) and maintenance nivolumab (six cycles, q3w).

Main Outcome Measure:

Complete metabolic response of primary site and metastases on imaging, recovery of cranial neuropathies.

Results:

Following palliative radiation therapy and induction nivolumab, cranial neuropathies resolved. With maintenance-dose nivolumab, primary site and metastases exhibited a complete response. Therapy was stopped at 16 months post-diagnosis. Complete remission was maintained until 22 months after diagnosis. The patient developed a solitary cerebral metastasis which was refractory to radiosurgery and biopsy confirmed melanoma. He expired 2 years, 8 months post-diagnosis.

Conclusions:

Mucosal melanoma of the middle ear and petrous temporal bone is exceedingly rare. Management is individualized and surgery is undertaken when possible. Key observations in this case are the complete metabolic response and reversal of cranial nerve neuropathies following radiation and anti-programed cell death receptor ligand 1 therapy. Non-surgical treatment is worthy of study as initial management for similar lesions.
Heritability analysis of liver stiffness detected by ultrasound shear wave elastography: a twin study
Authors: Fekete Marton , Piroska Marton , Szily Marcell , Erdei Mercedesz , Jokkel Zsofia , Szabo Helga , Littvay Levente , Baffy Gyorgy , Tarnoki Adam Domonkos , Tarnoki David Laszlo
Published: July 2021

Objectives of the study

Nonalcoholic fatty liver disease (NAFLD) is a common condition with a subset of individuals developing liver fibrosis as a major risk factor for advanced liver disease. The contribution of genetic factors to this progression remains incompletely understood. Our aim was to analyze heritability in the development of liver fibrosis estimated by ultrasound shear wave elastography (SWE) in an asymptomatic adult twin cohort.

Methods

In total 172 adult Hungarian twins (51 monozygotic and 36 dizygotic pairs; 63% women; mean age 54.9 ± 15.1 years) underwent B-mode ultrasonography to assess steatosis and SWE to determine Young’s modulus as a noninvasive marker or liver fibrosis.

Results

We identified 99 subjects with steatosis, which was mild in 46 subjects (46%), moderate in 52 subjects (52%) and severe in a single subject (1%). Mean Young’s modulus was 7.58 ± 3.53 kPa in this slightly overweight study cohort (BMI: 25.7 ± 4.6 kg/m2). Univariate analysis adjusted for age, sex and BMI indicated no discernible role for genetic components in the presence of liver stiffness, whereas shared and unshared environmental effects accounted for 38.3% (95% confidence interval (CI), 17–56.1%) and 61.7% (95% CI, 43.9–83%).

Conclusions

Our findings do not support the heritability of liver stiffness in an asymptomatic, twin cohort with slight overweight and variable degree of steatosis, underscoring the importance of environmental factors in the development of NAFLD and liver fibrosis.
Chlorhexidine Mouthwash Fails to Eradicate Oropharyngeal Gonorrhea in a Clinical Pilot Trial (MoNg)
Authors: Van Dijck Christophe , Tsoumanis Achilleas , De Hondt Annelies , Cuylaerts Vicky , Laumen Jolein , Van Herrewege Yven , Florence Eric , De Baetselier Irith , Kenyon Chris
Published: July 2021

This single-arm open-label pilot trial in Antwerp, Belgium, was ended early in accordance with the protocol because twice-daily gargling with chlorhexidine 0.2% for 6 days failed to eradicate Neisseria gonorrhoeae from the oropharynx of asymptomatic men who have sex with men (n = 3; efficacy of 0%; 95% confidence interval, 0%–56.1%).
HER2 Testing: Insights From Pathologists’ Perspective on Technically Challenging HER2 FISH Cases
Authors: Grimm Erin V. , Allison Kimberly H. , Hicks David G. , Swenson Karen K. , Krueger Janet , Yaziji Hadi , Downs-Kelly Erinn , Rendi Mara H. , Susnik Barbara , Tsai Michaela L. , Lillemoe Tamera J.
Published: July 2021

Objective:

College of American Pathologists and the American Society of Clinical Oncology guidelines provide straightforward criteria for HER2 interpretation in breast carcinomas; however, a subset of cases present unusual diagnostic dilemmas.

Materials and Methods:

Ten challenging HER2 fluorescence in situ hybridization (FISH) cases were selected for analysis. The study included a variety of problematic cases such as those with discordant immunohistochemistry (IHC) and FISH results, cases with high intratumoral variability in HER2 copy number, a case with a highly amplified clone in 5% to 10% of the tumor sample, and a case with tumor cells containing tightly clumped HER2 signals. Six high volume HER2 FISH laboratories performed and interpreted HER2 FISH (adding HER2 IHC if necessary). Interpretation strategies were discussed.

Results:

There was 100% concordance between laboratories in 4/10 cases. Tumors with increased intratumoral variability (tumors with high variability in HER2 copy number per cell but which otherwise do not fulfill College of American Pathologists and the American Society of Clinical Oncology criteria for heterogeneity) exhibited 100% concordance in 3/4 cases, but 1 case had only 50% agreement. Low positive HER2 cases (group 1 cases with <6 average HER2 copies/cell) had 1 laboratory disagreeing with the majority in 4/4 cases, and this was the only category with discordance between IHC and FISH methodologies. All laboratories identified the case with heterogeneity and interpreted it as positive. Five of the 6 laboratories interpreted the case with tightly clustered HER2 signals as positive.

Conclusions:

This study offers specific observations and interpretation strategies that laboratories can use when confronted with difficult HER 2 cases. It then highlights communication strategies a laboratory may use to discuss these unusual HER2 results with the clinical team.
The limitations of hospital and law enforcement databases in characterizing the epidemiology of firearm injury
Authors: Miller Keith R. , Egger Michael E. , Pike Annabelle , Burden Jennifer , Bozeman Matthew C. , Franklin Glen A. , Nash Nicholas A. , Smith Jason W. , Harbrecht Brian G. , Benns Matthew V.
Published: July 2021

BACKGROUND

Current data on the epidemiology of firearm injury in the United States are incomplete. Common sources include hospital, law enforcement, consumer, and public health databases, but each database has limitations that exclude injury subgroups. By integrating hospital (inpatient and outpatient) and law enforcement databases, we hypothesized that a more accurate depiction of the totality of firearm injury in our region could be achieved.

METHODS

We constructed a collaborative firearm injury database consisting of all patients admitted as inpatients to the regional level 1 trauma hospital (inpatient registry), patients treated and released from the emergency department (ED), and subjects encountering local law enforcement as a result of firearm injury in Jefferson County, Kentucky. Injuries recorded from January 1, 2016, to December 31, 2020, were analyzed. Outcomes, demographics, and injury detection rates from individual databases were compared with those of the combined collaborative database and compared using χ2 testing across databases.

RESULTS

The inpatient registry (n = 1,441) and ED database (n = 1,109) were combined, resulting in 2,550 incidents in the hospital database. The law enforcement database consisted of 2,665 patient incidents, with 2,008 incidents in common with the hospital database and 657 unique incidents. The merged collaborative database consisted of 3,207 incidents. In comparison with the collaborative database, the inpatient, total hospital (inpatient and ED), and law enforcement databases failed to include 55%, 20%, and 17% of all injuries, respectively. The hospital captured nearly 94% of survivors but less than 40% of nonsurvivors. Law enforcement captured 93% of nonsurvivors but missed 20% of survivors. Mortality (11–26%) and injury incidence were markedly different across the databases.

DISCUSSION

The utilization of trauma registry or law enforcement databases alone do not accurately reflect the epidemiology of firearm injury and may misrepresent areas in need of greater injury prevention efforts.

LEVEL OF EVIDENCE

Epidemiological, level IV.
Combined Metabolic Activators Improves Cognitive Functions in Alzheimer’s Disease
Authors: Yulug Burak , Altay Ozlem , Li Xiangyu , Hanoglu Lutfu , Cankaya Seyda , Lam Simon , Yang Hong , Coskun Ebru , İdil Ezgi , Nogaylar Rahim , Bayram Cemil , Bolat Ismail , Öner Sena , Tozlu Özlem Özdemir , Arslan Mehmet Enes , Hacımuftuoglu Ahmet , Yıldırım Serkan , Arif Muhammad , Shoaie Saeed , Zhang Cheng , Nielsen Jens , Turkez Hasan , Borén Jan , Uhlén Mathias , Mardinoglu Adil
Published: July 2021

Alzheimer’s disease (AD) is associated with metabolic abnormalities linked to critical elements of neurodegeneration. Here, we analysed the brain transcriptomics data of more than 600 AD patients using genome-scale metabolic models and provided supporting evidence of mitochondrial dysfunction related to the pathophysiologic mechanisms of AD progression. Subsequently, we investigated, in a rat model of AD, the oral administration of Combined Metabolic Activators (CMAs), consisting of NAD+ and glutathione precursors, to explore the effect for improvement of biological functions in AD. CMAs includes L-serine, nicotinamide riboside, N-acetyl-L-cysteine, and L-carnitine tartrate, salt form of L-carnitine. The study revealed that supplementation of the CMAs improved the AD-associated histological parameters in the animals. Finally, we designed a randomized, double-blinded, placebo-controlled human phase 2 clinical trial and showed that the administration of CMAs improves cognitive functions in AD patients. As decreased AD Assessment Scale-cognitive subscale (ADAS-Cog) score is the indicator of the improved cognitive function in AD patients, we observed a significant decrease of ADAS-Cog scores on Day 84 vs Day 0 (Log2FC= -0.37, (29% improvement), p-value=0.00001) in the CMA group. We also observed a significant decrease in the placebo group on Day 84 vs Day 0 (Log2FC= -0.19, (14% improvement), p-value=0.001) due to the recommendations of exercise and Mediterranean diet to all AD patients participated in the trial. A comprehensive analysis of the human plasma metabolome and proteome revealed that plasma levels of proteins and metabolites associated with redox metabolism are significantly improved after treatment. In conclusion, our results show that treating AD patients with CMAs leads to enhanced cognitive functions, suggesting a role for such a therapeutic regime in treating AD and other neurodegenerative diseases.

HIGHLIGHTS

•

Brain transcriptomics data of more than 600 AD patients is analysed.

•

Performed anin vivostudy using Combined Metabolic Activators (CMAs) in AD rat models.

•

We performed a randomized, double-blinded, placebo-controlled human phase 2 clinical trial.

•

We showed that cognitive functions in AD patients is improved 29% in the CMA group whereas 14% in the placebo group.
Association between telecommuting environment and low back pain among Japanese telecommuting workers: A cross-sectional study
Authors: Matsugaki Ryutaro , Muramatsu Keiji , Tateishi Seiichiro , Nagata Tomohisa , Tsuji Mayumi , Hino Ayako , Ikegami Kazunori , Fujino Yoshihisa , Matsuda Shinya
Published: July 2021

Objectives

We evaluated the relationship between telecommuting environment and low back pain (LBP) among desk-based workers in Japan.

Methods

This cross-sectional study included 3,663 desk-based, telecommuting workers. LBP was assessed using a 0–10 numerical rating scale. The telecommuting environment was evaluated using subjective questions. Mixed-effects logistic regression analysis was used to evaluate this association.

Results

The results of mixed-effects logistic model revealed that not having a place or room to concentrate on work, desk not well-lit enough for work, lack of space on the desk to work, not having enough legroom, and uncomfortable temperature and humidity conditions in the workspace were significantly associated with higher odds of LBP.

Conclusions

Our findings suggest that telecommuting environment is associated with the prevalence of LBP.
Real-time genomic surveillance during the 2021 re-emergence of the yellow fever virus in Rio Grande do Sul State, Brazil
Authors: Andrade M.S. , Campos F.S. , Campos A.A.S. , Abreu F.V.S. , Melo F.L. , Cardoso J.C. , Santos E. , Born L.C. , Silva C.M.D. , Müller N.F.D. , Oliveira C.H. , Silva A.J.J. , Simonini-Teixeira D. , Bernal-Valle S. , Mares-Guia M.A. , Albuquerque G.R. , Sevá A.P. , Romano A.P.M. , Franco A.C. , Ribeiro B.M. , Roehe P.M. , Almeida M.A.B.
Published: July 2021

The yellow fever virus (YFV) re-emergence in Rio Grande do Sul, Brazil, raised big concerns and led the state to declare a Public Health Emergency of State Importance. Here, we generated near-complete genomes from the ongoing outbreak in Southern Brazil, aiming to better understand the phylogenetic aspects and also spatio-temporal dynamics of the virus. Our findings highlight the path and dispersion in Rio Grande do Sul and that YFV was reintroduced from São Paulo to the Rio Grande do Sul state through Paraná and Santa Catarina states, at the end of 2020.
The diversity of quinoa morphological traits and seed metabolic composition
Authors: Tabatabaei Iman , Alseekh Saleh , Shahid Mohammad , Leniak Ewa , Wagner Mateusz , Mahmoudi Henda , Thushar Sumitha , Fernie Alisdair R , Murrphy Kevin M , Schmöckel Sandra M. , Tester Mark , Mueller-Roeber Bernd , Skirycz Aleksandra , Balazadeh Salma
Published: July 2021

Quinoa (Chenopodium quinoa Willd.) is an herbaceous annual crop of the amaranth family (Amaranthaceae). It is increasingly cultivated for its nutritious grains, which are rich in protein and essential amino acids, lipids, and minerals. Quinoa exhibits a high tolerance towards various abiotic stresses including drought and salinity, which supports its agricultural cultivation under climate change conditions. The use of quinoa grains is compromised by anti-nutritional saponins, a terpenoid class of secondary metabolites deposited in the seed coat; their removal before consumption requires extensive washing, an economically and environmentally unfavorable process; or their accumulation can be reduced through breeding. In this study, we analyzed the seed metabolomes, including amino acids, fatty acids, and saponins, from 471 quinoa cultivars, including two related species, by liquid chromatography-mass spectrometry. Additionally, we determined a large number of agronomic traits including biomass, flowering time, and seed yield. The results revealed considerable diversity between genotypes and provide a knowledge base for future breeding or genome editing of quinoa.
Genomic epidemiology and strain taxonomy ofCorynebacterium diphtheriae
Authors: Guglielmini Julien , Hennart Melanie , Badell Edgar , Toubiana Julie , Criscuolo Alexis , Brisse Sylvain
Published: July 2021

Background

Corynebacterium diphtheriaeis highly transmissible and can cause large diphtheria outbreaks where vaccination coverage is insufficient. Sporadic cases or small clusters are observed in high-vaccination settings. The phylogeography and short timescale evolution ofC. diphtheriaeare not well understood, in part due to a lack of harmonized analytical approaches of genomic surveillance and strain tracking.

Methods

We combined 1,305 genes with highly reproducible allele calls into a core genome multilocus sequence typing (cgMLST) scheme. We analyzed cgMLST genes diversity among 602 isolates from sporadic clinical cases, small clusters or large outbreaks. We defined sublineages based on the phylogenetic structure withinC. diphtheriaeand strains based on the highest number of cgMLST mismatches within documented outbreaks. We performed time-scaled phylogenetic analyses of major sublineages.

Results

The cgMLST scheme showed high allele call rate inC. diphtheriaeand the closely related speciesC. belfantiiandC. rouxii. We demonstrate its utility to delineate epidemiological case clusters and outbreaks using a 25 mismatches threshold, and reveal a number of cryptic transmission chains, most of which are geographically restricted to one or a few adjacent countries. Subcultures of the vaccine strain PW8 differed by up to 20 cgMLST mismatches. Phylogenetic analyses revealed short timescale evolutionary gain or loss of the diphtheria toxin and biovar-associated genes. We devised a genomic taxonomy of strains and deeper sublineages (defined using a 500 cgMLST mismatches threshold), currently comprising 151 sublineages, only a few of which are geographically widespread based on current sampling. The cgMLST genotyping tool and nomenclature was made publicly accessible athttps://bigsdb.pasteur.fr/diphtheria.

Conclusions

Standardized genome-scale strain genotyping will help tracing transmission and geographic spread ofC. diphtheriae. The unified genomic taxonomy ofC. diphtheriaestrains provides a common language for studies into the ecology, evolution and virulence heterogeneity amongC. diphtheriaesublineages.
Xenogeneic Fibroblasts Inhibit The Growth Of Breast And Ovarian Cancer Cell Lines In Co-Culture
Authors: Usha Lydia , Klapko Oleksandra , Edassery Seby
Published: July 2021

Cell-based therapies cure some hematologic malignancies, although little information exists on solid cancer cell responses. The study objective was to test the hypothesis that xenogeneic fibroblasts can inhibit the growth of human cancer cell lines in vitro. Seven human cell lines (pancreatic cancer HPAF II; brain cancer U-87 MG; fibrosarcoma; ovarian cancer OVCAR3 and SKOV3; and breast cancer MCF7 and MDA-MB231) were co-cultured with two xenogeneic fibroblast cell lines (CV-1; monkey, Cercopithecus aethiops and DF-1; chicken, Gallus gallus) in a transwell culture system. Cancer cell proliferation was assessed colorimetrically. Different concentrations of breast and ovarian cancer cells were tested. Gene expression induced by DF-1 xenogeneic fibroblasts was assessed by RNAseq of MCF7 breast cancer cells. The proliferation of the majority of the cancer cell lines was altered by co-culture with xenogeneic fibroblasts. Cell proliferation was increased (4-17%) by CV-1; DF-1 increased brain cancer cell proliferation (16%), decreased breast and ovarian cancer cell growth (15 and 26% respectively) but did not affect fibrosarcoma and pancreatic cancer cells. When the initial cancer cell concentrations were lowered 4-fold, growth inhibition of breast and ovarian cancer increased more than 2-fold. DF-1 fibroblasts induced significant differential expression of 484 genes in MCF7 breast cancer cells; 285 genes were down-regulated and 199 genes were upregulated compared to control. Genes involved in the immune response were the major downregulated entities. RNAseq results were validated by qRT-PCR of 12 genes. The results show that xenogeneic fibroblasts can alter the growth and gene expression of cancer cells in vitro. This suggests a potentially novel investigational approach to the control of cancer cell growth.
Differential stimulation of pluripotent stem cell-derived human microglia leads to exosomal proteomic changes affecting neurons
Authors: Mallach Anna , Gobom Johan , Arber Charles , Piers Thomas M , Hardy John , Wray Selina , Zetterberg Henrik , Pocock Jennifer
Published: July 2021

Microglial exosomes are an emerging communication pathway, implicated in fulfilling homeostatic microglial functions and transmitting neurodegenerative signals. Gene variants of the triggering receptor expressed myeloid cells-2 (TREM2) are associated with an increased risk of developing dementia. We investigated the influence of the TREM2 Alzheimer’s disease risk variant, R47Hhet, on the microglial exosomal proteome consisting of 3019 proteins secreted from human iPS-derived microglia (iPS-Mg). Exosomal protein content changed according to how iPS-Mg were stimulated. Thus lipopolysaccharide (LPS) induced microglial exosomes to contain more inflammatory signals, whilst stimulation with the TREM2 ligand phosphatidylserine (PS+) increased metabolic signals within the microglial exosomes. We tested the effect of these exosomes on neurons and found that the exosomal protein changes were functionally relevant and influenced downstream functions in both neurons and microglia. Exosomes from R47Hhet iPS-Mg contained disease-associated microglial (DAM) signature proteins, and were less able to promote outgrowth of neuronal processes and increase mitochondrial metabolism in neurons compared with exosomes from TREM2 common variant iPS-Mg. Taken together these data highlight the importance of microglial exosomes in fulfilling microglial functions. Additionally, variations in the exosomal proteome influenced by the R47HhetTREM2 variant may underlie the increased risk of Alzheimer’s disease associated with this variant.

Graphical Abstract
Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data
Authors: Phaneuf Patrick V. , Zielinski Daniel C. , Yurkovich James T. , Johnsen Josefin , Szubin Richard , Yang Lei , Kim Se Hyeuk , Schulz Sebastian , Wu Muyao , Dalldorf Christopher , Ozdemir Emre , Palsson Bernhard O. , Feist Adam M.
Published: July 2021

Microbes are being engineered for an increasingly large and diverse set of applications. However, the designing of microbial genomes remains challenging due to the general complexity of biological system. Adaptive Laboratory Evolution (ALE) leverages nature’s problem-solving processes to generate optimized genotypes currently inaccessible to rational methods. The large amount of public ALE data now represents a new opportunity for data-driven strain design. This study presents a novel and first of its kind meta-analysis workflow to derive data-driven strain designs from aggregate ALE mutational data using rich mutation annotations, statistical and structural biology methods. The mutational dataset consolidated and utilized in this study contained 63 Escherichia coli K-12 MG1655 based ALE experiments, described by 93 unique environmental conditions, 357 independent evolutions, and 13,957 observed mutations. High-level trends across the entire dataset were established and revealed that ALE-derived strain designs will largely be gene-centric, as opposed to non-coding, and a relatively small number of variants (approx. 4) can significantly alter cellular states and provide benefits which range from an increase in fitness to a complete necessity for survival. Three novel experimentally validated designs relevant to metabolic engineering applications are presented as use cases for the workflow. Specifically, these designs increased growth rates with glycerol as a carbon source through a point mutation to glpK and a truncation to cyaA or increased tolerance to toxic levels of isobutyric acid through a pykF truncation. These results demonstrate how strain designs can be extracted from aggregated ALE data to enhance strain design efforts.

Abstract Figure
CRISPR screens for host factors critical for infection by SARS-CoV-2 variants of concern identify GATA6 as a central modulator of ACE2
Authors: Israeli Ma’ayan , Finkel Yaara , Yahalom-Ronen Yfat , Paran Nir , Chitlaru Theodor , Israeli Ofir , Cohen-Gihon Inbar , Aftalion Moshe , Falach Reut , Elia Uri , Nemet Ital , Kliker Limor , Mandelboim Michal , Beth-Din Adi , Israely Tomer , Cohen Ofer , Stern-Ginossar Noam , Bercovich-Kinori Adi
Published: July 2021

The global spread of SARS-CoV-2 led to the most challenging pandemic in this century, posing major economic and health challenges worldwide. Revealing host genes essential for infection by multiple variants of SASR-CoV-2 can provide insights into the virus pathogenesis, and facilitates the development of novel broad-spectrum host-directed therapeutics. Here, employing genome-scale CRISPR screens, we provide a comprehensive data-set of cellular factors that are exploited by WT-SARS-CoV-2 as well as two additional recently emerged variants of concerns (VOCs), Alpha and Beta. These screens identified known and novel host factors critical for SARS-CoV-2 infection, including various components belonging to the Clathrin-dependent transport pathway, ubiquitination and Heparan sulfate biogenesis. In addition, the host phosphatidylglycerol biosynthesis processes appeared to have major anti-viral functions. Comparative analysis of the different VOCs revealed the host factors KREMEN2 and SETDB1 as potential unique candidates required only to the Alpha variant, providing a possible explanation for the increased infectivity of this variant. Furthermore, the analysis identified GATA6, a zinc finger transcription factor, as an essential pro-viral gene for all variants inspected. We revealed that GATA6 directly regulates ACE2 transcription and accordingly, is critical for SARS-CoV-2 cell entry. Analysis of clinical samples collected from SARS-CoV-2 infected individuals showed an elevated level of GATA6, indicating the important role GATA6 may be playing in COVID-19 pathogenesis. Finally, pharmacological inhibition of GATA6 resulted in down-modulation of ACE2 and consequently to inhibition of the viral infectivity. Overall, we show GATA6 represents a target for the development of anti-SARS-CoV-2 therapeutic strategies and reaffirm the value of the CRISPR loss-of-function screens in providing a list of potential new targets for therapeutic interventions.
Intramembrane protease SPP defines a cholesterol-regulated abundance control of the mevalonate pathway enzyme SQS
Authors: Avci Dönem , Heidasch Ronny , Costa Martina , Lüchtenborg Christian , Kale Dipali , Brügger Britta , Lemberg Marius K.
Published: July 2021

Intramembrane proteolysis regulates important processes such as signaling and transcriptional and posttranslational abundance control of proteins with key functions in metabolic pathways. This includes transcriptional control of mevalonate pathway genes, thereby ensuring balanced biosynthesis of cholesterol and other isoprenoids. Our work shows that, at high cholesterol levels, signal peptide peptidase (SPP) cleaves squalene synthase (SQS), an enzyme that defines the branching point for allocation of isoprenoids to the sterol and non-sterol arms of the mevalonate pathway. This intramembrane cleavage releases SQS from the membrane and targets it for proteasomal degradation. Regulation of this mechanism is achieved by the E3 ubiquitin ligase TRC8 that, in addition to ubiquitinating SQS in response to cholesterol levels, acts as an allosteric activator of SPP-catalyzed intramembrane cleavage of SQS. Cellular cholesterol levels increase in the absence of SPP activity. Hence, SPP-TRC8 mediated abundance control of SQS acts as a regulation step within the mevalonate pathway.
A dynamic and combinatorial histone code drives malaria parasite asexual and sexual development
Authors: von Grüning Hilde , Coradin Mariel , Mendoza Mariel R. , Reader Janette , Sidoli Simone , Garcia Benjamin A. , Birkholtz Lyn-Marie
Published: July 2021

A ‘histone code’ defines system-level crosstalk between histone post-translational modifications (PTMs) to induce specific biological outcomes. Proteome-scale information of co-existing PTM across the entire chromatin landscape of the malaria parasite, Plasmodium falciparum, was lacking. Here, we used advanced quantitative middle-down proteomics to identify combinations of PTMs in both the proliferative, asexual stages and transmissible, sexual gametocyte stages of P. falciparum. We provide an updated, high-resolution compendium of 72 PTMs on H3 and H3.3, of which 30 are novel to the parasite. Co-existing PTMs with unique stage distinction was identified, indicating a dynamic and complex histone code with increased connectivity of novel PTMs seen in gametocytes. Chromatin proteomics of a gametocyte-specific combination, H3R17me2K18acK23ac, identified a SAGA-like effector complex (including the transcription factor AP2-G2) tied to this combination to regulate gene expression in mature gametocytes. Ultimately, this study unveils previously undiscovered histone PTMs and their functional relationship with co-existing partners. These results highlight that investigating chromatin regulation in the parasite using single histone PTM assays might overlook higher order gene regulation for distinct proliferation and differentiation processes.
Inference of polyploid origin and inheritance mode from population genomic data
Authors: Scott Alison Dawn , Van de Velde Jozefien D. , Novikova Polina Yu.
Published: July 2021

Summary/Abstract

Whole-genome duplications yield varied chromosomal pairing patterns, ranging from strictly bivalent to multivalent, resulting in disomic and polysomic inheritance modes. In the bivalent case, homeologous chromosomes form pairs, where in a multivalent pattern all copies are homologous and are therefore free to pair and recombine. As sufficient sequencing data is more readily available than high-quality cytological assessments of meiotic behavior or population genetic assessment of allelic segregation, especially for non-model organisms, here we describe two bioinformatics approaches to infer origins and inheritance modes of polyploids using short-read sequencing data. The first approach is based on distributions of allelic read depth at the heterozygous sites within an individual, as the expectations of such distributions are different for disomic and polysomic inheritance modes. The second approach is more laborious and based on a phylogenetic assessment of partially phased haplotypes of a polyploid in comparison to the closest diploid relatives. We discuss the sources of deviations from expected inheritance patterns, advantages and pitfalls of both methods, effects of mating types on the performance of the methods, and possible future developments.
Phytoene synthase 2 in tomato fruits remains functional and contributes to abscisic acid formation
Authors: Gupta Prateek , Rodriguez-Franco Marta , Bodanapu Reddaiah , Sreelakshmi Yellamaraju , Sharma Rameshwar
Published: July 2021

In ripening tomato fruits, the leaf-specific carotenoids biosynthesis mediated by phytoene synthase 2 (PSY2) is replaced by a fruit-specific pathway by the expression of two chromoplast-specific genes: phytoene synthase 1 (PSY1) and lycopene-β-cyclase (CYCB). Though both PSY1 and PSY2 genes express in tomato fruits, the functional role of PSY2 is not known. To decipher whether PSY2-mediated carotenogenesis operates in ripening fruits, we blocked the in vivo activity of lycopene-β-cyclases in fruits of several carotenoids and ripening mutants by CPTA (2-(4-Chlorophenylthio)triethylamine hydrochloride), an inhibitor of lycopene-β-cyclases. The CPTA-treatment induced accumulation of lycopene in leaves, immature-green and ripening fruits. Even, in psy1 mutants V7 and r that are deficient in fruit-specific carotenoid biosynthesis, CPTA triggered lycopene accumulation but lowered the abscisic acid level. Differing from fruit-specific carotenogenesis, CPTA-treated V7 and r mutant fruits accumulated lycopene but not phytoene and phytofluene. The lack of phytoene and phytofluene accumulation was reminiscent of PSY2-mediated leaf-like carotenogenesis, where phytoene and phytofluene accumulation is never seen. The lycopene accumulation was associated with the partial transformation of chloroplasts to chromoplasts bearing thread-like crystalline structures. Our study uncovers the operation of a parallel carotenogenesis pathway mediated by PSY2 that provides precursors for abscisic acid biosynthesis in ripening tomato fruits.

Significance statement

It is believed that in ripening tomato fruits phytoene synthase 2 that drives carotenoid biosynthesis in leaves is redundant. Contrary to this, we show that in phytoene synthase 1 mutant fruit that is bereft of lycopene, the chemical inhibition of lycopene β-cyclases triggers lycopene accumulation. Our results uncover that phytoene synthase 2 remains functional in ripening fruits and provides precursors for abscisic acid formation in fruits.
Single-cell RNA Sequencing Reveals the Temporal Diversity and Dynamics of Cardiac Immunity after Myocardial Infarction
Authors: Jin Kaiyu , Gao Shan , Yang Penghui , Guo Rongfang , Li Dan , Zhang Yunsha , Lu Xiaoyan , Fan Guanwei , Fan Xiaohui
Published: July 2021

Myocardial infarction (MI) is strongly associated with the temporal regulation of cardiac immunity. However, a variety of current clinical trials have failed because of the lack of post-MI immunomodulating/anti-inflammatory targets. We performed single-cell RNA sequencing analysis of cardiacCd45+immune cell at 0, 3, 7, and 14 days after injury in a mouse left anterior descending coronary artery ligation model. Major immune cell populations, distinct subsets, and dynamic changes were identified. Macrophages (Mø)/monocytes were most abundant, peaking at 3 days after infarction. Mø-5 and Mø-6 were the predominant infiltrated subsets at this time point, with strong expression of inflammatory factors. Further analysis demonstrated that suppressing these sets attenuated pathological MI progression by preventing subsequent leukocyte extravasation and adverse remodeling. We also detected abundant apoptotic neutrophils and a profibrotic macrophage subset on days 7 and 14 respectively. These results provide a basis for developing cell type- and time-specific interventions in MI.

Graphic abstract

Temporal regulation of cardiac immunity is strongly associated with the onset, progression, and outcomes of MI. Our study of time-series scRNA-seq on the whole cardiac immune cells isolated from the LAD ligation mice and the tanshinone IIA treated mice shed light on the underlying pathology of MI.
Typical and disrupted brain circuitry for conscious awareness in full-term and preterm infants
Authors: Hu Huiqing , Cusack Rhodri , Naci Lorina
Published: July 2021

One of the great frontiers of consciousness science is understanding how early consciousness arises in the development of the human infant. The reciprocal relationship between the default mode network (DMN) and frontoparietal networks — the dorsal attention network (DAN) and executive control network (ECN) — is thought to facilitate integration of information across the brain and its availability for conscious access to a wide set of mental operations. It remains unknown whether the brain mechanism of conscious awareness is instated in infants from birth. To address this gap, we asked what the impact of prematurity and neonate age is on the development the default mode and fronto-parietal networks, and of their reciprocal relationship. To address these questions, we used the Developing Human Connectome Project (dHCP), a unique Open Science project which provides a large sample of neonatal functional Magnetic Resonance Imaging (fMRI) data with high temporal and spatial resolution. Resting state fMRI data for full-term neonates (N = 282, age 41.2 w ± 12 d), and preterm neonates scanned at term-equivalent age (TEA) (N = 73, 40.9 w ± 14.5 d), or before TEA (N = 73, 34.6 w ± 13.4 d) were obtained from the dHCP, and for a reference adult group (N = 176, 22 – 36 years), from the Human Connectome Project. For the first time, we show that the reciprocal relationship between the DMN and DAN was present at full-term birth or TEA. Although different from the adult networks, the DMN, DAN and ECN were present as distinct networks at full-term birth or TEA, but premature birth disrupted network development. By contrast, neonates before TEA showed dramatic underdevelopment of high-order networks. Only the DAN was present as a distinct network and the reciprocal network relationship was not yet formed. Our results suggest that, at full-term birth or by term-equivalent age, infants possess key features of the neural circuitry that enables integration of information across diverse sensory and high-order functional modules, giving rise to conscious access. Conversely, they suggest that this brain infrastructure is not present before infants reach term-equivalent age. These findings improve understanding of the ontogeny of high-order network dynamics that support conscious awareness, and of their disruption by premature birth.
CHOmpact: a reduced metabolic model of Chinese hamster ovary cells with enhanced interpretability
Authors: Jiménez del Val Ioscani , Kyriakopoulos Sarantos , Albrecht Simone , Stockmann Henning , Rudd Pauline M , Polizzi Karen M , Kontoravdi Cleo
Published: July 2021

Metabolic modelling has emerged as a key tool for the characterisation of biopharmaceutical cell culture processes. Metabolic models have also been instrumental in identifying genetic engineering targets and developing feeding strategies that optimise the growth and productivity of Chinese hamster ovary (CHO) cells. Despite their success, metabolic models of CHO cells still present considerable challenges. Genome scale metabolic models (GeMs) of CHO cells are very large (>6000 reactions) and are, therefore, difficult to constrain to yield physiologically consistent flux distributions. The large scale of GeMs also makes interpretation of their outputs difficult. To address these challenges, we have developed CHOmpact, a reduced metabolic network that encompasses 101 metabolites linked through 144 reactions. Our compact reaction network allows us to deploy multi-objective optimisation and ensure that the computed flux distributions are physiologically consistent. Furthermore, our CHOmpact model delivers enhanced interpretability of simulation results and has allowed us to identify the mechanisms governing shifts in the anaplerotic consumption of asparagine and glutamate as well as an important mechanism of ammonia detoxification within mitochondria. CHOmpact, thus, addresses key challenges of large-scale metabolic models and, with further development, will serve as a platform to develop dynamic metabolic models for the control and optimisation of biopharmaceutical cell culture processes.
SOX4 facilitates PGR protein stability and FOXO1 expression conducive for human endometrial decidualization
Authors: Huang Pinxiu , Deng Wenbo , Bao Haili , Lin Zhong , Liu Mengying , Wu Jinxiang , Zhou Xiaobo , Qiao Manting , Yang Yihua , Cai Han , Rao Faiza , Chen Jingsi , Chen Dunjin , Lu Jinhua , Wang Haibin , Qin Aiping , Kong Shuangbo
Published: July 2021

The establishment of receptive endometrium in human necessitates appropriate decidualization of stromal cells, which involves steroids regulated periodic transformation of endometrial stromal cells during menstrual cycle. Insufficient decidualization of endometrium contributes to not only the failure of embryo implantation and unexplained infertility, but also the occurrence of recurrent spontaneous abortion, intrauterine growth retardation, preeclampsia, and other clinical gynecological diseases. However, the potential molecular regulatory mechanism underlying the initiation and maintenance of decidualization in humans is yet to be fully elucidated. In this investigation, we document that SOX4 is a key regulator of human endometrial stromal cells (hESCs) decidualization by directly regulating PRL and FOXO1 expression as revealed by whole genomic binding of SOX4 assay and RNA-Seq. Besides, our immunoprecipitation and mass spectrometry results unravel that SOX4 modulates progesterone receptor (PGR) stability through repressing E3 ubiquitin ligase HERC4 mediated degradation. More importantly, we provide evidence that dysregulated SOX4-HERC4-PGR axis is a potential cause of defective decidualization and recurrent implantation failure (RIF) in IVF patients. In summary, this study evidences that SOX4 is a new and critical regulator for human endometrial decidualization, and provides insightful information for the pathology of decidualization-related infertility and will pave the way for pregnancy improvement.
Genetic basis of enhanced stress resistance in long-lived mutants highlights key role of innate immunity in determining longevity
Authors: Soo Sonja K. , Rudich Paige D. , Mistry Meeta , Van Raamsdonk Jeremy M.
Published: July 2021

Mutations that extend lifespan are associated with enhanced resistance to stress. To better understand the molecular mechanisms underlying this relationship, we studied nine long-lived C. elegans mutants representative of different pathways of lifespan extension. We directly compared the magnitude of their lifespan extension and their ability to resist various external stressors (heat, oxidative stress, bacterial pathogens, osmotic stress, and anoxia). Furthermore, we analysed gene expression in each of these mutants to identify genes and pathways responsible for the enhanced resistance to stress. All of the examined long-lived mutants have increased resistance to one or more type of stress. Resistance to each of the examined types of stress had a significant, positive correlation with lifespan, with bacterial pathogen resistance showing the strongest relationship. All of the examined long-lived mutants have significant upregulation of multiple stress response pathways but differ in which stress response pathway has the greatest enrichment of genes. We used RNA sequencing data to identify which genes are most highly correlated with each type of stress resistance. There was a highly significant overlap between genes highly correlated with stress resistance, and genes highly correlated with longevity, suggesting that the same genetic pathways drive both phenotypes. This was especially true for genes correlated with bacterial pathogen resistance, which showed an 84% overlap with genes correlated with lifespan. Overall, our results demonstrate a strong correlation between stress resistance and longevity that results from the high degree of overlap in genes contributing to each phenotype.

SIGNIFICANCE STATEMENT

While increased resistance to stress has been correlated with longevity, the genetic basis for this relationship is incompletely understood. To advance our understanding of the relationship between stress resistance and lifespan, we measured lifespan, stress resistance and gene expression in a panel of nine long-lived mutants in C. elegans. All of the long-lived mutants exhibit enhanced resistance to at least one external stressor resulting from significant upregulation of multiple stress response pathways. Importantly, our data indicates that the same genetic pathways control stress resistance and lifespan, thereby accounting for the strong correlation between these two phenotypes. This work demonstrates the importance of innate immune signaling and other stress response pathways in determining longevity.