bluuebunny/crossref_metadata_2025 huggingface dataset:
Bringing Gender-Affirming Care to Primary Care
Authors: Mueller Rebecca C. , DeSimone M. Elayne
Published: April 2023

Background:

An increasing number of individuals who identify as transgender and gender diverse require informed and compassionate health care, yet there is a dearth of research about which educational strategies are best used to provide nurses and nurse practitioners the foundation upon which to provide appropriate health care.

Purpose:

This study evaluated a multimodal approach that included guided readings, a transgender patient panel, standardized patient simulation, and group discussion.

Methods:

The Sexual Orientation Counselor Competency Scale was administered pre- and postintervention.

Results:

Results demonstrated increases in knowledge, skills, and attitudes among the 16 participants. A high level of satisfaction was expressed for the overall program, but especially for the patient panel and standardized patient encounter.

Conclusions:

Nurse educators are encouraged to include information about health care of the transgender patient into curricula.
Understanding Factors Influencing Decision Making by State Health Officials in a Public Health Emergency
Authors: Barishansky Raphael M. , Fraser Michael R.
Published: April 2023

State and territorial health officials (STHOs) play a critical role in leading public health emergency response in their respective states. Through an exploratory qualitative study with 21 current or former STHOs, we sought to understand the issues that impact STHO decision making in public health responses. Initial findings suggest the need for structured decision making tools for use by leaders responding to public health emergencies, including COVID-19. Such tools could lead to more systematic responses by STHOs during public health crises.
Adverse Patient Safety Events During the COVID-19 Epidemic
Authors: Yackel Edward E. , Knowles Regina , Jones Carol M. , Turner James , Pendley Louis Robin , Mazzia Lisa M. , Mills Peter D.
Published: May 2023

The coronavirus disease 2019 (COVID-19) epidemic has exposed vulnerabilities within the U.S. healthcare system and globally. This study reviewed COVID-related high-harm patient safety events in the Veterans Health Administration to further our knowledge of the effects of the COVID-19 pandemic on patient safety.

Methods

A retrospective descriptive analysis of patient safety events related to COVID-19 was performed on data that were submitted in the Joint Patient Safety Event Reporting System and Root Cause Analysis databases to the VHA National Center for Patient Safety from March 2020 to February 2021. Events were coded for type of event, location, and cause of event.

Results

Delays in care and staff/patients exposed to COVID-19 were the most common types of patient safety events, followed by COVID-19–positive patients eloping, laboratory processing errors, and one wrong procedure. The most frequently cited locations where events took place were emergency departments, medical units, community living centers, and intensive care units. Confusion over procedures, care not provided because of COVID-19, and failure to identify COVID-positive patient before they exposed others to COVID were the most common causes for patient safety events.

Discussion

Our results are similar to other studies of patient safety during the first year of the COVID-19 pandemic. Based on these results, we recommend the following: (1) focus on patient safety culture, leadership, and governance; (2) proactively develop competency checklists, cognitive aids, and other tools for healthcare staff who are working in new or unfamiliar clinical settings; (3) augment or enhance communication efforts with patient safety huddles or briefings at all levels within a healthcare organization to proactively uncover risk and mitigate fear by explaining changes in policies and procedures; and (4) maximize the use of quality and patient safety experts who are knowledgeable in system and human factor theories as well as change management to assist in redesigning clinical workflows and processes.
Repair of Congenital Enlarged Parietal Foramina With Porous Polyethylene Implants
Authors: Wallace Robert D. , Uygur Safak , Konofaos Petros , Klimo Paul
Published: May 2023

Enlarged biparietal foramina is an autosomal dominant disorder that is caused by a failure of completion of ossification within the parietal bones. Enlarged parietal foramina measuring more than a few millimeters are uncommon. Even though spontaneous regression has been described, closure is rarely complete, and depending on the size of the resulting defect, an unprotected brain is a concern. There are few reports on the surgical management of persistent enlarged biparietal foramina. This is the first report describing our experience with a custom porous polyethylene implant.
Intracranial Neuro-Enteric Cyst
Authors: Zheng Junfei , Yan Xuelei , Ma Yongqian , Tao Xiaowei , Qin Shiqiang
Published: April 2023

An intracranial nerve-enteric cyst is a relatively rare benign disease, and the main clinical manifestations are related to the location and size of the cyst. The main symptoms are caused by cyst compression. When the cyst is small without compression, it may have no obvious symptoms, and when the cyst increases to a certain degree, it may cause corresponding clinical manifestations. The diagnosis of this disease is mainly based on clinical manifestations, imaging examinations, and pathological examinations. The authors present a 47-year-old woman who was admitted to the hospital with “dizziness”. Imaging was performed and revealed a small round lesion in the posterior cranial fossa in front of the brainstem. It was surgically removed and the postoperative pathology revealed an intracranial neuro-enteric cyst. The patient’s dizziness disappeared after surgery and was reviewed 1 year later without recurrence.
Serum Angiotensin-Converting Enzyme Methylation Level and Its Significance in Patients With Comorbid Major Depressive Disorder and Hypertension
Authors: Abula Gulibakeranmu , Li Jinxian , Ma Rui , Zhang Tin , Aji Adila , Zhang Yi
Published: April 2023

Objective

Major depressive disorder (MDD) often coexists with hypertension (HYT). DNA methylation has elicited vital functionality in their development. Angiotensin-converting enzyme (ACE) is a vital enzyme in blood pressure. This study investigated the effect of ACE methylation on depression and HYT severity in patients with comorbid MDD and HYT (MDD + HYT).

Methods

A total of 119 patients (41 men, 78 women, average age: 56.8 ± 9.1 years) with MDD + HYT were enrolled, with 89 healthy subjects (29 men, 60 women, average age: 57.4 ± 9.7 years) were enrolled. The Hamilton Depression Rating Scale-17 and self-rating depression scale scoring scales were used to assess the depression degree of patients, serum ACE methylation level in MDD + HYT patients was measured by means of bisulfite sequencing polymerase chain reaction, with subsequent analysis of the diagnostic efficacy of ACE methylation for MDD + HYT. The independent risk factors for sMDD + HYT were explored.

Results

Serum ACE methylation levels were significantly increased in MDD + HYT patients. The area under the curve of serum ACE methylation level for accurate diagnosis of MDD + HYT was 0.8471, and the cut-off value was 26.9 (sensitivity 83.19%, specificity 73.03%). ACE methylation was an independent risk factor for sMDD + HYT (P = 0.014; odds ratio, 1.071; 95% confidence interval = 1.014–1.131).

Conclusion

The elevated serum ACE methylation level (P < 0.001) in patients with MDD + HYT elicited definite diagnostic values for MDD + HYT, and ACE methylation level was independently correlated with sMDD + HYT (P < 0.05).
Human leukocyte antigen F-associated transcript 10 regulates the

I
Ks

potassium channel by competing for Kv7.1 ubiquitination
Authors: Chen Chen , Zhu Xin , Xie Jinyan , Li Xiaoqing , Wan Rong , Hong Kui
Published: May 2023

The protein expression and function changes from the slow-delayed rectifying
K
+
current,

I
Ks

, are tightly associated with ventricular cardiac arrhythmias. Human leukocyte antigen F-associated transcript 10 (FAT10), a member of the ubiquitin-like-modifier family, exerts a protective effect against myocardial ischaemia. However, whether or how FAT10 influences the function of

I
Ks

remains unclear. Here, human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) and
Fat10
knockout HEK293 (

Fat10
−/−

) cells through CRISPR-Cas9 technology were used to evaluate the novel modulation of FAT10 in

I
Ks

function. Patch-clamp studies showed that the overexpression of FAT10 significantly enhanced the current density of

I
Ks

both in hiPSC-CMs and HEK293-

Fat10
−/−

cells. In addition, a shortened action potential duration (APD) was seen from hiPSC-CMs transfected with the
ad-Fat10
virus. Then, a series of molecular approaches from neonatal rat cardiomyocytes, H9C2 cells and HEK293 cells were used to determine the regulatory mechanism of FAT10 in

I
Ks

. First, western blot assays indicated that the expression of Kv7.1, the alpha-subunit of

I
Ks

, was increased when FAT10 was overexpressed. Furthermore, immunofluorescence and co-immunoprecipitation assays demonstrated that FAT10 could interact with Kv7.1. Notably, FAT10 impedes Kv7.1 ubiquitination and degradation, thereby stabilizing its expression. Finally, a hypoxia model of hiPSC-CMs was established, and the overexpression of FAT10 showed a protective effect against hypoxia-induced decreases in the current density of

I
Ks

. Taken together, these findings revealed a novel role of FAT10 in the regulation of the

I
Ks

potassium channel by competing for Kv7.1 ubiquitination, which provides a new electrophysiological insight that FAT10 could modulate Kv7.1.

This article is part of the theme issue ‘The heartbeat: its molecular basis and physiological mechanisms’.
Timing mechanisms to control heart rhythm and initiate arrhythmias: roles for intracellular organelles, signalling pathways and subsarcolemmal Ca2+
Authors: Terrar Derek A.
Published: May 2023

Rhythms of electrical activity in all regions of the heart can be influenced by a variety of intracellular membrane bound organelles. This is true both for normal pacemaker activity and for abnormal rhythms including those caused by early and delayed afterdepolarizations under pathological conditions. The influence of the sarcoplasmic reticulum (SR) on cardiac electrical activity is widely recognized, but other intracellular organelles including lysosomes and mitochondria also contribute. Intracellular organelles can provide a timing mechanism (such as an SR clock driven by cyclic uptake and release of Ca2+, with an important influence of intraluminal Ca2+), and/or can act as a Ca2+store involved in signalling mechanisms. Ca2+plays many diverse roles including carrying electric current, driving electrogenic sodium–calcium exchange (NCX) particularly when Ca2+is extruded across the surface membrane causing depolarization, and activation of enzymes which target organelles and surface membrane proteins. Heart function is also influenced by Ca2+mobilizing agents (cADP-ribose, nicotinic acid adenine dinucleotide phosphate and inositol trisphosphate) acting on intracellular organelles. Lysosomal Ca2+release exerts its effects via calcium/calmodulin-dependent protein kinase II to promote SR Ca2+uptake, and contributes to arrhythmias resulting from excessive beta-adrenoceptor stimulation. A separate arrhythmogenic mechanism involves lysosomes, mitochondria and SR. Interacting intracellular organelles, therefore, have profound effects on heart rhythms and NCX plays a central role.

This article is part of the theme issue ‘The heartbeat: its molecular basis and physiological mechanisms’.
Compendium of clinical variant classification for 2,247 uniqueABCA4variants to improve genetic medicine access for Stargardt Disease
Authors: Cornelis Stéphanie S. , Bauwens Miriam , Haer-Wigman Lonneke , De Bruyne Marieke , Pantrangi Madhulatha , De Baere Elfride , Hufnagel Robert B. , Dhaenens Claire-Marie , Cremers Frans P.M.
Published: April 2023

Biallelic variants inABCA4cause Stargardt disease (STGD1), the most frequent heritable macular disease. Determination of the pathogenicity of variants inABCA4proves to be difficult due to 1) the high number of benign and pathogenic variants in the gene; 2) the presence of complex alleles; 3) the extensive variable expressivity of this disease and 4) reduced penetrance of hypomorphic variants. Therefore, the classification of many variants inABCA4is currently of uncertain significance. Here we complemented theABCA4Leiden Open Variation Database (LOVD) with data from ∼11,000 probands withABCA4-associated inherited retinal diseases from literature up to the end of 2020. We carefully adapted the ACMG/AMP classifications toABCA4and assigned these classifications to all 2,247 unique variants from theABCA4LOVD to increase the knowledge of pathogenicity. In total, 1,247 variants were categorized with a Likely Pathogenic or Pathogenic classification, whereas 194 variants were categorized with a Likely Benign or Benign classification. This uniform and improved structured reclassification, incorporating the largest dataset ofABCA4-associated retinopathy cases so far, will improve both the diagnosis as well as genetic counselling for individuals withABCA4-associated retinopathy.
Long-read genome assembly of the insect model organismTribolium castaneumreveals spread of satellite DNA in gene-rich regions by recurrent burst events
Authors: Marin Volarić , Evelin Despot-Slade , Damira Veseljak , Brankica Mravinac , Nevenka Meštrović
Published: April 2023

Eukaryotic genomes are replete with satellite DNAs (satDNAs), large stretches of tandemly repeated sequences which are mostly underrepresented in genome assemblies. Here we combined Nanopore long-read sequencing with a reference-guided assembly approach, to generate an improved, high-quality genome assembly TcasONT of the model beetleTribolium castaneum. Enriched by 45 Mb in the repetitive part, the new assembly comprises almost the entire genome sequence. We used the enhanced assembly to conduct global and in-depth analyses of abundant euchromatic satDNAs, Cast1-Cast9. Contrary to the commonly adopted view, our finding showed the extensive spread of satDNAs in gene-rich regions, including long arrays. The results of the principal component analysis of monomers and sequence similarity relationships between satDNA arrays, revealed an occurrence of recent satDNAs array exchange between different chromosomes. We proposed a scenario of their genome dynamics characterized by repeated bursts of satDNAs spreading through euchromatin, followed by a process of elongation and homogenization of arrays. We also found that suppressed recombination on the X chromosome has no significant effect on the spread of satDNAs, but rather tolerates the amplification of these satDNAs into longer arrays. Analyses of arrays’ neighboring regions showed a tendency of one Cast satDNA to be associated with transposon-like elements. Using 2D electrophoresis followed by Southern blotting, we proved Cast satDNAs presence in the fraction of extrachromosomal circular DNA (eccDNA). We point to two mechanisms that enable the said satDNA spread to occur: transposition by transposable elements and insertion mediated by eccDNA. The presence of such a large proportion of satDNA in gene-rich regions inevitably gives rise to speculation about their possible influence on gene expression.
Genomewide association study of epiretinal membrane: discovery of significant risk loci in each of three American populations
Authors: Gelernter Joel , Levey Daniel , Galimberti Marco , Harrington Kelly , Zhou Hang , Adhikari Keyrun , Gaziano J. Michael , Eliott Dean , Stein Murray B.
Published: April 2023

IMPORTANCE

Epiretinal membrane (ERM) is a common retinal condition characterized by the presence of fibrocellular tissue on the retinal surface, often with consequent loss of vision and visual distortion.

OBJECTIVE

Genomewide association studies (GWAS) can reveal the biology underlying complex genetic traits like ERM; there have been no previous large-scale GWAS of this trait.

DESIGN

We used electronic health record diagnosis to identify Million Veteran Program (MVP) participants with ERM in three populations for genomewide association analysis and further statistical investigation of the results.

SETTING

Veterans who volunteered for the nationwide Department of Veterans Affairs MVP study, eligible because they have used Veterans Health Administration facilities

PARTICIPANTS

31,374 European-American (EUR) cases and 414,052 EUR controls, 4,739 African-American (AFR) cases and 107,773 AFR controls, and 2,119 Latino (Admixed American, AMR) cases and 36,163 AMR controls – a total of 38,232 cases and 557,988 controls.

METHODS

We completed GWAS in each population separately, then results were meta-analyzed. We also evaluated genetic correlation with other traits in external samples, and completed pathway enrichment analyses.

MAIN OUTCOME MEASURES

Genomewide-significant association with ERM.

RESULTS

Genomewide significant associations were observed in all three populations studied: 31 risk loci in EUR subjects, 3 in AFR, and 2 in AMR, with 48 identified in trans-ancestry meta-analysis. The most strongly associated locus in both EUR (rs9823832, p=9.06×10−37) and the meta-analysis (rs28630834, p=2.90×10−37) wasDHX36(DEAH-Box Helicase 36). We investigated expression quantitative trait locus associations for eye related function and found several GWS variants associate to alterations in gene expression in the macula, includingDHX36*rs9438. ERM showed significant genetic correlation to depression and to disorders of the vitreous. Pathway enrichment analyses implicated collagen and collagen-adjacent mechanisms, among others.

CONCLUSIONS AND RELEVANCE

This well-powered ERM GWAS has identified novel genetic associations, some very strong, that point to biological mechanisms for ERM and merit further investigation.
A Linear Mixed Model with Measurement Error Correction (LMM-MEC): A Method for Summary-data-based Multivariable Mendelian Randomization
Authors: Ding Ming , Zou Fei
Published: April 2023

Summary-data-based multivariable Mendelian randomization (MVMR) methods, such as MVMR-Egger, MVMR-IVW, MVMR median-based, and MVMR-PRESSO, assess the causal effects of multiple risk factors on disease. However, accounting for variances in summary statistics related to risk factors remains a challenge. We propose a linear mixed model with measurement error correction (LMM-MEC) that accounts for the variance of summary statistics for both disease outcomes and risk factors. In step I, a linear mixed model is applied to account for the variance in disease summary statistics. Specifically, if heterogeneity is present in disease summary statistics, we treat it as a random effect and adopt an iteratively re-weighted least squares algorithm to estimate causal effects. In step II, we treat the variance in the summary statistics of risk factors as multiple measurement errors and apply a regression calibration method for simultaneous multiple measurement error correction. In a simulation study, when using independent genetic variants as instrumental variables (IV), our method showed comparable performance to existing MVMR methods under conditions of no pleiotropy or balanced pleiotropy with the outcome, and it exhibited higher coverage rates and power under directional pleiotropy. Similar findings were observed when using genetic variants with low to moderate linkage disequilibrium (LD) (0 <ρ2≤ 0.3) as IVs, although coverage rates reduced for all methods compared to using independent genetic variants as IVs. In the application study, we examined causal associations between correlated cholesterol biomarkers and longevity. By including 739 genetic variants selected based on P values <5×10-5from GWAS and allowing for low LD (ρ2≤ 0.1), our method identified that large LDL-c were causally associated with lower likelihood of achieving longevity.
Clinical value of cortical bursting in preterm infants with intraventricular haemorrhage
Authors: Koskela Tuomas , Meek Judith , Huertas-Ceballos Angela , Kendall Giles S , Whitehead Kimberley
Published: April 2023

Objective

In healthy preterm infants, cortical burst rate and temporal dynamics predict important measures such as brain growth. We hypothesised that in preterm infants with germinal matrix-intraventricular haemorrhage (GM-IVH), cortical bursting could provide prognostic information. We determined how cortical bursting was influenced by the injury, and whether this was related to developmental outcome.

Methods

We identified 47 EEGs from 33 infants with GM-IVH ≥grade II (median gestational age: 25 weeks), acquired between 24-40 weeks corrected gestational age as part of routine clinical care. In a subset of 33 EEGs from 25 infants with asymmetric injury, we used the least-affected hemisphere as an internal control. We tested whether cortical burst rate predicted death or severe motor impairment (median 2 years follow-up; range 1-2 years corrected).

Results

GM-IVH depressed central cortical burst rate. Bursts over the worst-affected hemisphere were less likely to immediately follow (within 1 second) bursts over the least-affected hemisphere than vice versa. Lower burst rate was modestly associated with death or severe motor impairment (specificity 93%, sensitivity 37%).

Conclusions

EEG can quantitatively index the functional injury after GM-IVH.

Significance

Higher cortical burst rate is reassuring for a positive motor outcome over the first 2 years.

Highlights

GM-IVH depresses cortical burst rate

GM-IVH unbalances inter-hemispheric burst dynamics

Higher burst rate following GM-IVH is associated with positive motor outcome at median 2 years
Tumor cell heterogeneity drives spatial organization of the intratumoral immune response in squamous cell skin carcinoma
Authors: Tanaka Miho , Lum Lotus , Hu Kenneth , Ledezma-Soto Cecilia , Samad Bushra , Superville Daphne , Ng Kenneth , Adams Zoe , Kersten Kelly , Fong Lawrence , Combes Alexis J. , Krummel Matthew , Reeves Melissa
Published: April 2023

Intratumoral heterogeneity (ITH)—defined as genetic and cellular diversity within a tumor—is linked to failure of immunotherapy and an inferior anti-tumor immune response. The underlying mechanism of this association is unknown. To address this question, we modeled heterogeneous tumors comprised of a pro-inflammatory (“hot”) and an immunosuppressive (“cold”) tumor population, labeled with YFP and RFP tags respectively to enable precise spatial tracking. The resulting mixed-population tumors exhibited distinct regions comprised of YFP+(hot) cells, RFP+(cold) cells, or a mixture. We found that tumor regions occupied by hot tumor cells (YFP+) harbored more total T cells and a higher frequency of Th1 cells and IFNγ+CD8 T cells compared to regions occupied by cold tumor cells (RFP+), whereas immunosuppressive macrophages showed the opposite spatial pattern. We identified the chemokine CX3CL1, produced at higher levels by our cold tumors, as a mediator of intratumoral macrophage accumulation, particularly immunosuppressive CD206Himacrophages. Furthermore, we examined the response of heterogeneous tumors to a therapeutic combination of PD-1 blockade and CD40 agonist on a region-by-region basis. While the combination successfully increases Th1 abundance in “cold” tumor regions, it fails to bring overall T cell activity to the same level as seen in “hot” regions. The presence of the “cold” cells thus ultimately leads to a failure of the therapy to induce tumor rejection. Collectively, our results demonstrate that the organization of heterogeneous tumor cells has a profound impact on directing the spatial organization and function of tumor-infiltrating immune cells as well as on responses to immunotherapy.
COP9 signalosome complex subunit-7-mediated regulation of cAMP levels contributes to autophagic degradation and pathogenesis of rice blast fungusMagnaporthe oryzae
Authors: Lin Lili , Guo Hengyuan , Batool Wajjiha , Lin Lianyu , Cao Jiayin , An Qiuli , Aliyu Sami Rukaiya , Bao Jiandong , Wang Zonghua , Norvienyeku Justice
Published: May 2023

Photo-dependent processes, including circadian rhythm, autophagy, ubiquitination, neddylation/deneddylation, and metabolite biosynthesis, profoundly influence microbial pathogenesis. Although a photomorphogenesis signalosome (COP9/CSN) has been identified, the mechanism by which this large complex contributes to pathophysiological processes in filamentous fungi remains unclear.

Here, we identified eight CSN complex subunits in the rice blast fungusMagnaporthe oryzaeand functionally characterized the translocon subunits containing a nuclear export or localization signal (NES/NLS).

Targeted gene replacement of these CSN subunits, includingMoCSN3,MoCSN5,MoCSN6,MoCSN7, andMoCSN12, attenuated vegetative growth and conidiation inM. oryzaeand rendered non-pathogenic deletion strains.MoCSN7deletion significantly suppressed arachidonic acid catabolism, compromised cell wall integrity, subverted photo-dependent ubiquitination, and abolished photo-responsiveness. Surprisingly, we also discovered that MoCSN subunits, particularly MoCsn7, are required for the cAMP-dependent regulation of autophagic flux.

Therefore, MoCSN significantly contributes to morphological, physiological, and pathogenic differentiation inM. oryzaeby fostering cross-talk between multiple pathways.
The mechanics of correlated variability in segregated cortical excitatory subnetworks
Authors: Negrón Alex , Getz Matthew P. , Handy Gregory , Doiron Brent
Published: April 2023

Understanding the genesis of shared trial-to-trial variability in neural activity within sensory cortex is critical to uncovering the biological basis of information processing in the brain. Shared variability is often a reflection of the structure of cortical connectivity since this variability likely arises, in part, from local circuit inputs. A series of experiments from segregated networks of (excitatory) pyramidal neurons in mouse primary visual cortex challenge this view. Specifically, the across-network correlations were found to be larger than predicted given the known weak cross-network connectivity. We aim to uncover the circuit mechanisms responsible for these enhanced correlations through biologically motivated cortical circuit models. Our central finding is that coupling each excitatory subpopulation with a specific inhibitory subpopulation provides the most robust network-intrinsic solution in shaping these enhanced correlations. This result argues for the existence of excitatory-inhibitory functional assemblies in early sensory areas which mirror not just response properties but also connectivity between pyramidal cells.
Self-regulatory function of bacterial small heat shock protein IbpA through mRNA binding is conferred by a conserved arginine
Authors: Cheng Yajie , Miwa Tsukumi , Taguchi Hideki
Published: April 2023

Bacterial small heat shock proteins, IbpA and IbpB, co-aggregate with denatured proteins and recruit other chaperones for the processing of aggregates, thereby assisting in their refolding. In addition, as a recently revealed uncommon feature,Escherichia coliIbpA self-represses its own translation through interaction with the 5’ untranslated region (UTR) of theibpAmRNA, enabling IbpA to act as a mediator of negative feedback regulation. Although IbpA also suppresses the expression of IbpB, IbpB does not have the self-repression activity despite the two Ibps being highly homologous. This study demonstrates that the self-repression function of IbpA is conserved in other bacterial IbpAs. Moreover, a cationic residue-rich region in the α-crystallin domain (ACD) of IbpA, which is not conserved in IbpB, is critical for the self-suppression activity. Notably, arginine 93 (R93) located within the ACD is an essential residue that cannot be replaced by the other 19 amino acids, including lysine. IbpA-R93 mutants completely lost the interaction with the 5’ UTR of theibpAmRNA but retained almost all of the chaperone activity to sequester denatured proteins. Taken together, the conserved Arg93-mediated translational control of IbpA through RNA binding would be beneficial for a rapid and massive supply of the chaperone on demand.
Inositol hexakisphosphate kinase 1 is essential for cell junction integrity in the mouse seminiferous epithelium
Authors: Bhat Sameer Ahmed , Malla Aushaq Bashir , Oddi Vineesha , Sen Jayraj , Bhandari Rashna
Published: April 2023

Inositol hexakisphosphate kinases (IP6Ks) are enzymes that catalyse the synthesis of the inositol pyrophosphate 5-IP7 which is involved in the regulation of many physiological processes in mammals. The IP6K paralog IP6K1 is expressed at high levels in the mammalian testis, and its deletion leads to sterility in male mice. Here, we show that the loss of IP6K1 in mice causes a delay in the first wave of spermatogenesis. Testes from juvenileIp6k1knockout mice show downregulation of transcripts that are involved in cell adhesion and formation of the testis-specific inter-Sertoli cell impermeable junction complex known as the blood-testis barrier (BTB). We demonstrate that loss of IP6K1 in the mouse testis causes BTB disruption associated with transcriptional misregulation of the tight junction protein claudin 3, and subcellular mislocalization of the gap junction protein connexin 43. In addition to BTB disruption, we also observe loss of germ cell adhesion in the seminiferous epithelium ofIp6k1knockout mice, ultimately resulting in premature sloughing of round spermatids into the epididymis. Mechanistically, we show that loss of IP6K1 in the testis enhances cofilin activity due to increased AKT/ERK and integrin signalling, resulting in destabilization of the actin-based cytoskeleton in Sertoli cells and germ cell loss.
GraphComm: A Graph-based Deep Learning Method to Predict Cell-Cell Communication in single-cell RNAseq data
Authors: So Emily , Hayat Sikander , Nair Sisira Kadambat , Wang Bo , Haibe-Kains Benjamin
Published: April 2023

Interactions between cells coordinate various functions across cell-types in health and disease states. Novel single-cell techniques enable deep investigation of cellular crosstalk at single-cell resolution. Cell-cell communication (CCC) is mediated by underlying gene-gene networks, however most current methods are unable to account for complex interactions within the cell as well as incorporate the effect of pathway and protein complexes on interactions. This results in the inability to infer overarching signalling patterns within a dataset as well as limit the ability to successfully explore other data types such as spatial cell dimension. Therefore, to represent transcriptomic data as intricate networks, complementing gene expression with information from cells to ligands and receptors for relevant cell-cell communication inference, we present GraphComm - a new graph-based deep learning method for predicting cell-cell communication in single-cell RNAseq datasets. GraphComm improves CCC inference by capturing detailed information such as cell location and intracellular signalling patterns from a database of more than 30,000 protein interaction pairs. With this framework, GraphComm is able to predict biologically relevant results in datasets previously validated for CCC, datasets that have undergone chemical or genetic perturbations and datasets with spatial cell information.
Analysis of single-cell CRISPR perturbations indicates that enhancers act multiplicatively and provides limited evidence for epistatic-like interactions
Authors: Zhou Jessica , Guruvayurappan Karthik , Toneyan Shushan , Chen Hsiuyi V. , Chen Aaron R. , Koo Peter , McVicker Graham
Published: April 2023

A single gene may have multiple enhancers, but how they work in concert to regulate transcription is poorly understood. To analyze enhancer interactions throughout the genome, we developed a generalized linear modeling framework, GLiMMIRS, for interrogating enhancer effects from single-cell CRISPR experiments. We applied GLiMMIRS to a published dataset and tested for interactions between 46,166 enhancer pairs and corresponding genes, including 264 ’high-confidence’ enhancer pairs. We found that enhancer effects combine multiplicatively but with limited evidence for further interactions. Only 31 enhancer pairs exhibited significant interactions (FDR < 0.1), of which none came from the high confidence subset and 20 were driven by outlier expression values. Additional analyses of a second CRISPR dataset and in silico enhancer perturbations with Enformer both support a multiplicative model of enhancer effects without interactions. Altogether, our results indicate that enhancer interactions are uncommon or have small effects that are difficult to detect.

Highlights

Analysis of a large single-cell CRISPRi screen finds limited evidence for synergistic or redundant interactions between enhancers

The collective action of multiple enhancers on a common target gene follows a multiplicative model of activity

A new statistical framework for simulating and modeling data from single-cell CRISPRi screens
Detection of dynamic lung hyperinflation using cardiopulmonary exercise testing and respiratory function in patients with stable cardiac disease: a multicenter cross-sectional study
Authors: Kominami Kazuyuki , Noda Kazuki , Minagawa Nanaho , Yonezawa Kazuya , Ueda Masanori , Kobayashi Yasuyuki , Murata Makoto , Akino Masatoshi
Published: May 2023

Background

Many patients with heart disease potentially have comorbid COPD, however there are not enough opportunities for screening and the qualitative differentiation of shortness of breath (SOB) has not been well established. We investigated the detection rate of SOB based on a visual and qualitative dynamic lung hyperinflation (DLH) detection index during cardiopulmonary exercise testing (CPET) and whether there was a difference in respiratory function between the two groups.

Methods

We recruited 534 patients with heart disease and to scrutinize physical functions (369 males, 67.0±12.9 years) who underwent CPET and spirometry simultaneously. The difference between inspiratory and expiratory tidal volume was calculated (TV E-I) from the breath-by-breath data. A TV E-I decrease after the start of exercise comprised the convex group, and a TV E-I that remained unchanged or increased comprised the non-convex group.

Results

129 patients (24.2%) were in the convex; there was no difference in clinical characteristics between groups. The Borg scale scores at the end of the CPET showed no difference. VE/VCO2 slope, its Y-intercept and minimum VE/VCO2 showed no significant difference. In the convex group, FEV1.0% was significantly lower (69.4±13.1 vs. 75.0±9.0%), and FEV1.0% and Y-intercept and the difference between minimum VE/VCO2 and VE/VCO2 slope were significantly correlated (r=−0.343 and r=−0.478).

Conclusions

The convex group showed decreased respiratory function, suggesting potential airway obstruction during exercise. A combined assessment of the TV E-I and Y-intercept of the VE/VCO2 slope or the difference between the minimum VE/VCO2 and VE/VCO2 slopes could potentially detect COPD or airway obstruction.
Analyzing bivariate cross-trait genetic architecture in GWAS summary statistics with the BIGA cloud computing platform
Authors: Li Yujue , Xue Fei , Li Bingxuan , Yang Yilin , Fan Zirui , Shu Juan , Yang Xiaochen , Wang Xiyao , Lin Jinjie , Copana Carlos , Zhao Bingxin
Published: May 2023

As large-scale biobanks provide increasing access to deep phenotyping and genomic data, genome-wide association studies (GWAS) are rapidly uncovering the genetic architecture behind various complex traits and diseases. GWAS publications typically make their summary-level data (GWAS summary statistics) publicly available, enabling further exploration of genetic overlaps between phenotypes gathered from different studies and cohorts. However, systematically analyzing high-dimensional GWAS summary statistics for thousands of phenotypes can be both logistically challenging and computationally demanding. In this paper, we introduce BIGA (https://bigagwas.org/), a website that aims to offer unified data analysis pipelines and processed data resources for cross-trait genetic architecture analyses using GWAS summary statistics. We have developed a framework to implement statistical genetics tools on a cloud computing platform, combined with extensive curated GWAS data resources. Through BIGA, users can upload data, submit jobs, and share results, providing the research community with a convenient tool for consolidating GWAS data and generating new insights.
SimpliPyTEM: An open-source Python library and app to simplify Transmission Electron Microscopy andin situ-TEM image analysis
Authors: Ing Gabriel , Stewart Andrew , Battaglia Guiseppe , Ruiz-Perez Lorena
Published: May 2023

Introducing SimpliPyTEM, a Python library and accompanying GUI that simplifies the post-acquisition evaluation of transmission electron microscopy (TEM) images, helping streamline the workflow. After an imaging session, a folder of image and/or video files, typically containing low contrast and large file size 32-bit images, can be quickly processed via SimpliPyTEM into high-quality, high-contrast .jpg images with suitably sized scale-bars. The app can also generate HTML or PDF files containing the processed images for easy viewing and sharing. Additionally, SimpliPyTEM has a specific focus on in situ TEM videos, an emerging field of EM, allowing for fast data processing into preview movies, averages, image series, or motion corrected averages using MotionCor2. The accompanying Python library offers many standard image processing methods, all simplified to a single command, plus a module to analyse particle morphology and population. This latter application is particularly useful for life sciences investigations. User-friendly tutorials and clear documentation are included to help guide users through the processing and analysis. We invite the EM community to contribute to and further develop this open-source package.
Molecular and morphological characterisation of four new ancyromonad genera and proposal for an updated taxonomy of the Ancyromonadida
Authors: Yubuki Naoji , Torruella Guifré , Galindo Luis Javier , Heiss Aaron A. , Ciobanu Maria Cristina , Shiratori Takashi , Ishida Ken-ichiro , Blaz Jazmin , Kim Eunsoo , Moreira David , López-García Purificación , Eme Laura
Published: May 2023

Ancyromonads are small biflagellated protists with a bean-shaped morphology. They are cosmopolitan in marine, freshwater and soil environments, where they attach to surfaces while feeding on bacteria. These poorly known grazers stand out by their uncertain phylogenetic position in the tree of eukaryotes, forming a deep-branching ‘orphan’ lineage that is considered key to better understanding the early evolution of eukaryotes. Despite their ecological and evolutionary interest, only limited knowledge exists about their true diversity. Here, we aimed to better characterise ancyromonads by integrating environmental surveys with behavioural observation and description of cell morphology, for which sample isolation and culturing is indispensable. We studied 18 ancyromonad strains, including 14 new isolates and 7 new species. Most of them belong to three new and genetically divergent genera:Caraotamonas,Nyramonas, andOlneymonas(encompassing 4 species). The remaining three new species belong to the already known generaFabomonasandAncyromonas. We also raisedStriomonas, formerly a subgenus ofNutomonas, to full genus status, based on morphological and phylogenetic grounds. For all these new species, we studied their morphology under light and electron microscopy and carried out molecular phylogenetic analyses, including as well 18S rRNA gene sequences from several environmental surveys. Based on these analyses, we have updated the taxonomy of Ancyromonadida.
ISRES+: An improved evolutionary strategy for function minimization to estimate the free parameters of Systems Biology models
Authors: Bandodkar Prasad U. , Shaikh Razeen R. , Reeves Gregory T.
Published: May 2023

Model development is essential to gain a mathematical understanding of the underlying phenomena in systems biology. In most models, it is typically hard to estimate the values of the biophysical/phenomenological parameters that characterize the model. The parameters are estimated by minimizing a function that reduces a measure of the error between model predictions and experimental data. In this work, we build on an algorithm for function minimization proposed by Runnarson and Yao, named Improved Evolutionary Strategy by Stochastic Ranking (ISRES), that finds a best-fit individual by evolving a population in the direction of minimizing error by using information at most from a pair of individuals in any generation to create a new population. Our algorithm, named ISRES+, builds on it by combining information from all individuals across the population and across all generations to gain a better sense of direction to evolve the population. ISRES+ makes use of the additional information generated by the creation of a large population in the evolutionary methods to approximate the local neighborhood around the best-fit individual using linear least squares fit in one and two dimensions. We compared the performance of the two algorithms on three systems biology models with varying complexities and found that not only does the ISRES+ lead to fitter individuals, but it also leads to a tighter distribution of fittest individuals over successive runs.
Multimodal engineering of extracellular vesicles for efficient intracellular protein delivery
Authors: Liang Xiuming , Gupta Dhanu , Xie Junhua , Wonterghem Elien Van , Hoecke Lien Van , Hean Justin , Niu Zheyu , Wiklander Oscar P. B , Zheng Wenyi , Wiklander Rim Jawad , He Rui , Mamand Doste R. , Bost Jeremy , Zhou Guannan , Zhou Houze , Roudi Samantha , Zickler Antje Maria , Gorgens Andre , Hagey Daniel , de Jong Olivier G. , Uy Aileen Geobee , Zong Yuanyuan , Mager Imre , Perez Carla Martin , Roberts Thomas C , Vader Pieter , Fougerolles Antonin de , Wood Matthew J. A. , Vandenbroucke Roosmarijn E , Nordin Joel Z. , EL Andaloussi Samir
Published: May 2023

Extracellular vesicles (EVs) are promising tools to transfer macromolecular therapeutic molecules to recipient cells, however, efficient functional intracellular protein delivery by EVs remains challenging. Here, we have developed novel and versatile systems that leverage selected molecular tools to engineer EVs for robust cytosolic protein delivery both in vitro and in vivo. These systems, termed VSV-G plus EV-sorting Domain-Intein-Cargo (VEDIC) and VSV-G-Foldon-Intein-Cargo (VFIC), exploit an engineered mini-intein (intein) protein with self-cleavage activity to link cargo to an EV-sorting domain and release it from the EV membrane inside the EV lumen. In addition, we utilize the fusogenic protein VSV-G to facilitate endosomal escape and cargo release from the endosomal system to the cytosol of recipient cells. Importantly, we demonstrate that the combination of the self-cleavage intein, fusogenic protein and EV-sorting domain are indispensable for efficient functional intracellular delivery of cargo proteins by engineered EVs. As such, nearly 100% recombination and close to 80% genome editing efficiency in reporter cells were observed by EV-transferred Cre recombinase and Cas9/sgRNA RNPs, respectively. Moreover, EV-mediated Cre delivery by VEDIC or VFIC engineered EVs resulted in significant in vivo recombination in Cre-LoxP R26-LSL-tdTomato reporter mice following both local and systemic injections. Finally, we applied these systems for improved treatment of LPS-induced systemic inflammation by delivering a super-repressor of NF-κB activity. Altogether, this study describes a platform by which EVs can be utilized as a vehicle for the efficient intracellular delivery of macromolecular therapeutics for treatments of disease.
FET fusion oncoproteins disrupt physiologic DNA repair networks in cancer
Authors: Menon Shruti , Gracilla Daniel , Breese Marcus R. , Lin Yone Phar , Cruz Filemon Dela , Feinberg Tamar , de Stanchina Elisa , Galic Ana-Florina , Allegakoen Hannah , Perati Shruthi , Wen Nicholas , Heslin Ann , Horlbeck Max A. , Weissman Jonathan , Sweet-Cordero E. Alejandro , Bivona Trever G. , Tulpule Asmin
Published: May 2023

While oncogenes promote cancer cell growth, unrestrained proliferation represents a significant stressor to cellular homeostasis networks such as the DNA damage response (DDR). To enable oncogene tolerance, many cancers disable tumor suppressive DDR signaling through genetic loss of DDR pathways and downstream effectors (e.g., ATM or p53 tumor suppressor mutations). Whether and how oncogenes can help “self-tolerize” by creating analogous functional defects in physiologic DDR networks is not known. Here we focus on Ewing sarcoma, a FET fusion oncoprotein (EWSR1-FLI1) driven pediatric bone tumor, as a model for the class of FET rearranged cancers. Native FET family members are among the earliest factors recruited to DNA double-strand breaks (DSBs), though the function of both native FET proteins and FET fusion oncoproteins in DNA repair remains to be defined. We discover that the EWSR1-FLI1 fusion oncoprotein is recruited to DNA DSBs and interferes with native FET (EWSR1) protein function in activating the DNA damage sensor ATM. In multiple FET rearranged cancers, FET fusion oncoproteins induce functional ATM defects, rendering the compensatory ATR signaling axis as a collateral dependency and therapeutic target. More generally, we find that aberrant recruitment of a fusion oncoprotein to sites of DNA damage can disrupt physiologic DSB repair, revealing a mechanism for how growth-promoting oncogenes can also create functional defects within tumor suppressive DDR networks.
Mechanisms controlling membrane recruitment and activation of autoinhibited SHIP1
Authors: Waddell Grace L. , Drew Emma E. , Rupp Henry P. , Hansen Scott D.
Published: May 2023

Signal transduction downstream of growth factor and immune receptor activation relies on the production of phosphatidylinositol-(3,4,5)-trisphosphate (PI(3,4,5)P3) lipids by phosphoinositide-3-kinase (PI3K). Regulating the strength and duration of PI3K signaling in immune cells, Src homology 2 domain-containing inositol 5-phosphatase 1 (SHIP1) controls the dephosphorylation of PI(3,4,5)P3to generate PI(3,4)P2. Although SHIP1 has been shown to regulate neutrophil chemotaxis, B-cell signaling, and cortical oscillations in mast cells, the role that lipid and protein interactions serve in controlling SHIP1 membrane recruitment and activity remains unclear. Using single molecule TIRF microscopy, we directly visualized membrane recruitment and activation of SHIP1 on supported lipid bilayers and the cellular plasma membrane. We find that SHIP1’s interactions with lipids are insensitive to dynamic changes in PI(3,4,5)P3both in vitro and in vivo. Very transient SHIP1 membrane interactions were detected only when membranes contained a combination of phosphatidylserine (PS) and PI(3,4,5)P3lipids. Molecular dissection reveals that SHIP1 is autoinhibited with the N-terminal SH2 domain playing a critical role in suppressing phosphatase activity. Robust SHIP1 membrane localization and relief of autoinhibition can be achieved through interactions with immunoreceptor derived phosphopeptides presented either in solution or conjugated to supported membranes. Overall, this work provides new mechanistic details concerning the dynamic interplay between lipid binding specificity, protein-protein interactions, and activation of autoinhibited SHIP1.