Association between a network-based physician linchpin score and cancer patient mortality: a SEER-Medicare analysis

BACKGROUND

Patients with cancer frequently require multidisciplinary teams for optimal cancer outcomes. Network analysis can capture relationships among cancer specialists, and we developed a novel physician linchpin score to characterize "linchpin" physicians whose peers have fewer ties to other physicians of the same oncologic specialty. Our study examined whether being treated by a linchpin physician was associated with worse survival.

METHODS

In this cross-sectional study, we analyzed Surveillance, Epidemiology, and End Results-Medicare data for patients diagnosed with stage I to III non-small cell lung cancer or colorectal cancer (CRC) in 2016-2017. We assembled patient-sharing networks and calculated linchpin scores for medical oncologists, radiation oncologists, and surgeons. Physicians were considered linchpins if their linchpin score was within the top 15% for their specialty. We used Cox proportional hazards models to examine associations between being treated by a linchpin physician and survival, with a 2-year follow-up period.

RESULTS

The study cohort included 10 081 patients with non-small cell lung cancer and 9036 patients with CRC. Patients with lung cancer treated by a linchpin radiation oncologist had a 17% (95% confidence interval = 1.04 to 1.32) greater hazard of mortality, and similar trends were observed for linchpin medical oncologists. Patients with CRC treated by a linchpin surgeon had a 22% (95% confidence interval = 1.03 to 1.43) greater hazard of mortality.

CONCLUSIONS

In an analysis of Medicare beneficiaries with nonmetastatic lung cancer or CRC, those treated by linchpin physicians often experienced worse survival. Efforts to improve outcomes can use network analysis to identify areas with reduced access to multidisciplinary specialists.

A genome assembly of the Yuma myotis bat, Myotis yumanensis

The Yuma myotis bat (Myotis yumanensis) is a small vespertilionid bat and one of 52 species of new world Myotis bats in the subgenus Pizonyx. While M. yumanensis populations currently appear relatively stable, it is one of 12 bat species known or suspected to be susceptible to white-nose syndrome, the fungal disease causing declines in bat populations across North America. Only two of these 12 species have genome resources available, which limits the ability of resource managers to use genomic techniques to track the responses of bat populations to white-nose syndrome generally. Here we present the first de novo genome assembly for Yuma myotis, generated as a part of the California Conservation Genomics Project. The M. yumanensis genome was generated using a combination of PacBio HiFi long reads and Omni-C chromatin-proximity sequencing technology. This high-quality genome is one of the most complete bat assemblies available, with a contig N50 of 28.03 Mb, scaffold N50 of 99.14 Mb, and BUSCO completeness score of 93.7%. The Yuma myotis genome provides a high-quality resource that will aid in comparative genomic and evolutionary studies, as well as inform conservation management related to white-nose syndrome.

Neural basis of speech and grammar symptoms in non-fluent variant primary progressive aphasia spectrum

The non-fluent/agrammatic variant of primary progressive aphasia (nfvPPA) is a neurodegenerative syndrome primarily defined by the presence of apraxia of speech (AoS) and/or expressive agrammatism. In addition, many patients exhibit dysarthria and/or receptive agrammatism. This leads to substantial phenotypic variation within the speech-language domain across individuals and time, in terms of both the specific combination of symptoms as well as their severity. How to resolve such phenotypic heterogeneity in nfvPPA is a matter of debate. 'Splitting' views propose separate clinical entities: 'primary progressive apraxia of speech' when AoS occurs in the absence of expressive agrammatism, 'progressive agrammatic aphasia' (PAA) in the opposite case, and 'AOS + PAA' when mixed motor speech and language symptoms are clearly present. While therapeutic interventions typically vary depending on the predominant symptom (e.g. AoS versus expressive agrammatism), the existence of behavioural, anatomical and pathological overlap across these phenotypes argues against drawing such clear-cut boundaries. In the current study, we contribute to this debate by mapping behaviour to brain in a large, prospective cohort of well characterized patients with nfvPPA (n = 104). We sought to advance scientific understanding of nfvPPA and the neural basis of speech-language by uncovering where in the brain the degree of MRI-based atrophy is associated with inter-patient variability in the presence and severity of AoS, dysarthria, expressive agrammatism or receptive agrammatism. Our cross-sectional examination of brain-behaviour relationships revealed three main observations. First, we found that the neural correlates of AoS and expressive agrammatism in nfvPPA lie side by side in the left posterior inferior frontal lobe, explaining their behavioural dissociation/association in previous reports. Second, we identified a 'left-right' and 'ventral-dorsal' neuroanatomical distinction between AoS versus dysarthria, highlighting (i) that dysarthria, but not AoS, is significantly influenced by tissue loss in right-hemisphere motor-speech regions; and (ii) that, within the left hemisphere, dysarthria and AoS map onto dorsally versus ventrally located motor-speech regions, respectively. Third, we confirmed that, within the large-scale grammar network, left frontal tissue loss is preferentially involved in expressive agrammatism and left temporal tissue loss in receptive agrammatism. Our findings thus contribute to define the function and location of the epicentres within the large-scale neural networks vulnerable to neurodegenerative changes in nfvPPA. We propose that nfvPPA be redefined as an umbrella term subsuming a spectrum of speech and/or language phenotypes that are closely linked by the underlying neuroanatomy and neuropathology.

Association between love breakup and suicidal ideation in Peruvian medical students: a cross-sectional study during the COVID-19 pandemic

Objective

We aimed to determine the association between a major romantic breakup and suicidal ideation in medical students from three universities in Peru.

Methods

A cross-sectional study was conducted during the first pandemic wave in 2021 on medical students from three universities in northern Peru. The outcome was suicidal ideation, measured with question nine of the Patient Health Questionnaire-9 (PHQ-9). Generalized Anxiety Disorder Scale-7 (GAD-7) and Insomnia Severity Index (ISI) were also used to assess mental health symptoms. The exposure was the experience of a major love breakup during the pandemic. In addition, its association with other covariates (age, sex, family members infected with COVID-19, deceased family members with COVID-19, insomnia, and anxiety, among others) was examined.

Results and discussions

Out of 370 students, 19.5% reported a major love breakup during the pandemic (95%CI: 15.5-23.8), and 34.3% had suicidal ideation (95%CI: 29.4-39.4). Having a major love breakup was associated with a higher prevalence of suicidal ideation (PR: 1.49, 95%CI: 1.32-1.67, p < 0.001). Moderate insomnia (PR: 2.56, 95%CI: 1.70-3.87, p < 0.001) and anxiety symptoms (PR: 1.94, 1.10-3.44, p = 0.023) were also associated with suicidal ideation.

Conclusion

Our study provides evidence of a significant association between a major love breakup and suicidal ideation. This finding emphasizes the need for further research to better understand this association and inform the development of effective suicide prevention policies in medical education.

Using a chat-based informed consent tool in large-scale genomic research

OBJECTIVE

We implemented a chatbot consent tool to shift the time burden from study staff in support of a national genomics research study.

MATERIALS AND METHODS

We created an Institutional Review Board-approved script for automated chat-based consent. We compared data from prospective participants who used the tool or had traditional consent conversations with study staff.

RESULTS

Chat-based consent, completed on a user's schedule, was shorter than the traditional conversation. This did not lead to a significant change in affirmative consents. Within affirmative consents and declines, more prospective participants completed the chat-based process. A quiz to assess chat-based consent user understanding had a high pass rate with no reported negative experiences.

CONCLUSION

Our report shows that a structured script can convey important information while realizing the benefits of automation and burden shifting. Analysis suggests that it may be advantageous to use chatbots to scale this rate-limiting step in large research projects.

The Varroa paradox: infestation levels and hygienic behavior in feral scutellata-hybrid and managed Apis mellifera ligustica honey bees

The Varroa destructor mite is a parasitic threat to managed and feral honey bee colonies around the world. Beekeepers use miticides to eliminate Varroa in commercial hives, but these chemicals can diminish bee health and increase miticide resistance. In contrast, feral honey bees have developed multiple ways to counteract mites without chemical treatment. We compared mite levels, grooming habits, and mite-biting behavior between feral Africanized honey bees (genomically verified Apis mellifera scutellata hybrids) and managed Italian honey bees (A. mellifera ligustica). Surprisingly, there was no difference in mite infestation levels between scutellata-hybrids and managed bees over one year despite the regular use of miticides in managed colonies. We also found no differences in the social immunity responses of the two groups, as measured by their hygienic habits (through worker brood pin-kill assays), self-grooming, and mite-biting behavior. However, we provide the first report that both scutellata-hybrids and managed honey bees bite off mite chemosensory forelegs, which the mites use to locate brood cells for reproduction, to a significantly greater degree than other legs (a twofold greater reduction in foreleg length relative to the most anterior legs). Such biting may impair mite reproduction.

Surface-active antibiotic production as a multifunctional adaptation for postfire microorganisms

Wildfires affect soils in multiple ways, leading to numerous challenges for colonizing microorganisms. Although it is thought that fire-adapted microorganisms lie at the forefront of postfire ecosystem recovery, the specific strategies that these organisms use to thrive in burned soils remain largely unknown. Through bioactivity screening of bacterial isolates from burned soils, we discovered that several Paraburkholderia spp. isolates produced a set of unusual rhamnolipid surfactants with a natural methyl ester modification. These rhamnolipid methyl esters (RLMEs) exhibited enhanced antimicrobial activity against other postfire microbial isolates, including pyrophilous Pyronema fungi and Amycolatopsis bacteria, compared to the typical rhamnolipids made by organisms such as Pseudomonas spp. RLMEs also showed enhanced surfactant properties and facilitated bacterial motility on agar surfaces. In vitro assays further demonstrated that RLMEs improved aqueous solubilization of polycyclic aromatic hydrocarbons, which are potential carbon sources found in char. Identification of the rhamnolipid biosynthesis genes in the postfire isolate, Paraburkholderia kirstenboschensis str. F3, led to the discovery of rhlM, whose gene product is responsible for the unique methylation of rhamnolipid substrates. RhlM is the first characterized bacterial representative of a large class of integral membrane methyltransferases that are widespread in bacteria. These results indicate multiple roles for RLMEs in the postfire lifestyle of Paraburkholderia isolates, including enhanced dispersal, solubilization of potential nutrients, and inhibition of competitors. Our findings shed new light on the chemical adaptations that bacteria employ to navigate, grow, and outcompete other soil community members in postfire environments.

Proteome trait regulation of marine Synechococcus elemental stoichiometry under global change

Recent studies have demonstrated regional differences in marine ecosystem C:N:P with implications for carbon and nutrient cycles. Due to strong co-variance, temperature and nutrient stress explain variability in C:N:P equally well. A reductionistic approach can link changes in individual environmental drivers with changes in biochemical traits and cell C:N:P. Thus, we quantified effects of temperature and nutrient stress on Synechococcus chemistry using laboratory chemostats, chemical analyses, and data-independent acquisition mass spectrometry proteomics. Nutrient supply accounted for most C:N:Pcell variability and induced tradeoffs between nutrient acquisition and ribosomal proteins. High temperature prompted heat-shock, whereas thermal effects via the "translation-compensation hypothesis" were only seen under P-stress. A Nonparametric Bayesian Local Clustering algorithm suggested that changes in lipopolysaccharides, peptidoglycans, and C-rich compatible solutes may also contribute to C:N:P regulation. Physiological responses match field-based trends in ecosystem stoichiometry and suggest a hierarchical environmental regulation of current and future ocean C:N:P.

Modulation of tooth regeneration through opposing responses to Wnt and BMP signals in teleosts

Most vertebrate species undergo tooth replacement throughout adult life. This process is marked by the shedding of existing teeth and the regeneration of tooth organs. However, little is known about the genetic circuitry regulating tooth replacement. Here, we tested whether fish orthologs of genes known to regulate mammalian hair regeneration have effects on tooth replacement. Using two fish species that demonstrate distinct modes of tooth regeneration, threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio), we found that transgenic overexpression of four different genes changed tooth replacement rates in the direction predicted by a hair regeneration model: Wnt10a and Grem2a increased tooth replacement rate, whereas Bmp6 and Dkk2 strongly inhibited tooth formation. Thus, similar to known roles in hair regeneration, Wnt and BMP signals promote and inhibit regeneration, respectively. Regulation of total tooth number was separable from regulation of replacement rates. RNA sequencing of stickleback dental tissue showed that Bmp6 overexpression resulted in an upregulation of Wnt inhibitors. Together, these data support a model in which different epithelial organs, such as teeth and hair, share genetic circuitry driving organ regeneration.

COVID-19-related stressors exacerbate food insecurity and depressive symptoms among graduate students receiving campus basic needs services: Cross-sectional findings from seven California public universities

Prior to the COVID-19 pandemic, food insecurity and depression were growing public health concerns among graduate students. Yet, little is known about how COVID-19-related stressors exacerbated these health outcomes among graduate students. To address this research gap, this study examined two types of COVID-19-related stressors, anticipated concerns about remote learning and challenges interfering with academic and research responsibilities, in relation to food insecurity and depressive symptoms among public university graduate students. Between August and October 2020, 631 graduate students who utilised basic needs services from seven University of California campuses completed an online survey assessing the effects of COVID-19 on their academic experiences, mental health, and basic needs security. Regression analyses examined associations of COVID-19-related concerns and COVID-19-related challenges with food insecurity as well as COVID-19-related concerns and COVID-19-related challenges in relation to depressive symptoms. All four models were adjusted for age, sex, race and ethnicity, campus affiliation, and living with a partner. Models examining food security status as the dependent variable were adjusted for depressive symptoms and vice versa. Graduate students concerned about delayed graduation, post-graduate employment, isolation from faculty and not having access to healthcare reported higher counts of depressive symptoms. Challenges associated with higher counts of depressive symptoms included caring for family more than usual, spending more time on errands and not paying for utilities in full. Students concerned about accessing healthcare had higher odds of experiencing food insecurity. Challenges associated with food insecurity included spending more time on errands, being unable to afford housing and sending money to family members during the pandemic. Our findings illuminate the pandemic's deleterious consequences on graduate students' mental health and food security, underscoring the need for strong academic and basic needs programs and policies.

The reference genome assembly of the bright cobblestone lichen, Acarospora socialis

Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been conducted on the genomics of A. socialis. To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. Lichen thallus tissue was collected from Pinkham Canyon in Joshua Tree National Park, California and deposited in the UC Riverside herbarium under accession #295874. The de novo assembly of the mycobiont partner of the lichen was generated from Pacific Biosciences HiFi long reads and Dovetail Omni-C chromatin capture data. After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. The BUSCO completeness score of the assembled genome was 97.5% using the Ascomycota gene set. Information on the genome of A. socialis is important for California conservation purposes given that this lichen is threatened in some places locally by wildfires due to climate change. This reference genome will be used for understanding the genetic diversity, population genomics, and comparative genomics of A. socialis species. Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California.

A draft reference genome assembly of the Pipevine Swallowtail butterfly, Battus philenor hirsuta

The California Pipevine Swallowtail Butterfly, Battus philenor hirsuta, and its host plant, the California Pipevine or Dutchman's Pipe, Aristolochia californica Torr., are an important California endemic species pair. While this species pair is an ideal system to study co-evolution, genomic resources for both are lacking. Here, we report a new, chromosome-level assembly of B. philenor hirsuta as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 109 scaffolds spanning 443 mega base (Mb) pairs, with a contig N50 of 14.6 Mb, a scaffold N50 of 15.2 Mb, and BUSCO complete score of 98.9%. In combination with the forthcoming A. californica reference genome, the B. philenor hirsuta genome will be a powerful tool for documenting landscape genomic diversity and plant-insect co-evolution in a rapidly changing California landscape.

Targeted Reversible Covalent Modification of a Noncatalytic Lysine of the Krev Interaction Trapped 1 Protein Enables Site-Directed Screening for Protein-Protein Interaction Inhibitors

The covalent reversible modification of proteins is a validated strategy for the development of probes and candidate therapeutics. However, the covalent reversible targeting of noncatalytic lysines is particularly challenging. Herein, we characterize the 2-hydroxy-1-naphthaldehyde (HNA) fragment as a targeted covalent reversible ligand of a noncatalytic lysine (Lys720) of the Krev interaction trapped 1 (KRIT1) protein. We show that the interaction of HNA with KRIT1 is highly specific, results in prolonged residence time of >8 h, and inhibits the Heart of glass 1 (HEG1)-KRIT1 protein-protein interaction (PPI). Screening of HNA derivatives identified analogs exhibiting similar binding modes as the parent fragment but faster target engagement and stronger inhibition activity. These results demonstrate that HNA is an efficient site-directing fragment with promise in developing HEG1-KRIT1 PPI inhibitors. Further, the aldimine chemistry, when coupled with templating effects that promote proximity, can produce a long-lasting reversible covalent modification of noncatalytic lysines.

Ocular Surface Regeneration by Limbal Stem Cells Therapies: State of the Art, Challenges, and Perspectives

Limbal stem cells (LSCs) are adult stem cells located at the limbus ensuring the continuous renewal of the corneal epithelium, critical to maintain an optimal visual function. Damages to the LSCs or their niche microenvironment lead to limbal stem cell deficiency (LSCD), a potentially blinding disease. Transplantation of LSCs as a treatment for severe to total LSCD has gained popularity since 1980s, owing to the clinical success of the first direct limbal autograft transplantation. Recent advances in the understanding of the LSCs' molecular identity and regulation have enabled preclinical and clinical advancements of promising LSCs therapies. However, lack of standardization of the diagnostic methods, staging of the disease severity, manufacturing process, and clinical outcome measures have hindered the advancement of the therapy. To move these therapies to the clinic, optimization and standardization of the diagnostic strategy, cell product manufacturing, and assessment of clinical efficacy with potency assays are key points to the development of customized therapies. Recent findings suggest that residual LSCs exist in eyes presenting with clinical signs of total LSCD, which opens new therapeutic strategies for eyes with partial LSCD. Prospective, randomized, multicentric controlled clinical trials are necessary to determine the efficacy of different LSCs therapies for different stages of LSCD using a set of standardized outcome measures.

Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations

Phylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have often relied on tools designed for de novo phylogenetic inference, in which all data are collected before any analysis is performed and the phylogeny is inferred once from scratch. SARS-CoV-2 data sets do not fit this mold. There are currently over 14 million sequenced SARS-CoV-2 genomes in online databases, with tens of thousands of new genomes added every day. Continuous data collection, combined with the public health relevance of SARS-CoV-2, invites an "online" approach to phylogenetics, in which new samples are added to existing phylogenetic trees every day. The extremely dense sampling of SARS-CoV-2 genomes also invites a comparison between likelihood and parsimony approaches to phylogenetic inference. Maximum likelihood (ML) and pseudo-ML methods may be more accurate when there are multiple changes at a single site on a single branch, but this accuracy comes at a large computational cost, and the dense sampling of SARS-CoV-2 genomes means that these instances will be extremely rare because each internal branch is expected to be extremely short. Therefore, it may be that approaches based on maximum parsimony (MP) are sufficiently accurate for reconstructing phylogenies of SARS-CoV-2, and their simplicity means that they can be applied to much larger data sets. Here, we evaluate the performance of de novo and online phylogenetic approaches, as well as ML, pseudo-ML, and MP frameworks for inferring large and dense SARS-CoV-2 phylogenies. Overall, we find that online phylogenetics produces similar phylogenetic trees to de novo analyses for SARS-CoV-2, and that MP optimization with UShER and matOptimize produces equivalent SARS-CoV-2 phylogenies to some of the most popular ML and pseudo-ML inference tools. MP optimization with UShER and matOptimize is thousands of times faster than presently available implementations of ML and online phylogenetics is faster than de novo inference. Our results therefore suggest that parsimony-based methods like UShER and matOptimize represent an accurate and more practical alternative to established ML implementations for large SARS-CoV-2 phylogenies and could be successfully applied to other similar data sets with particularly dense sampling and short branch lengths.

The maize preligule band is subdivided into distinct domains with contrasting cellular properties prior to ligule outgrowth

The maize ligule is an epidermis-derived structure that arises from the preligule band (PLB) at a boundary between the blade and sheath. A hinge-like auricle also develops immediately distal to the ligule and contributes to blade angle. Here, we characterize the stages of PLB and early ligule development in terms of topography, cell area, division orientation, cell wall rigidity and auxin response dynamics. Differential thickening of epidermal cells and localized periclinal divisions contributed to the formation of a ridge within the PLB, which ultimately produces the ligule fringe. Patterns in cell wall rigidity were consistent with the subdivision of the PLB into two regions along a distinct line positioned at the nascent ridge. The proximal region produces the ligule, while the distal region contributes to one epidermal face of the auricles. Although the auxin transporter PIN1 accumulated in the PLB, observed differential auxin transcriptional response did not underlie the partitioning of the PLB. Our data demonstrate that two zones with contrasting cellular properties, the preligule and preauricle, are specified within the ligular region before ligule outgrowth.

Consequences and Control of Multiscale Order/Disorder in Chiral Magnetic Textures

Transition metal intercalated transition metal dichalcogenides (TMDs) are promising platforms for next-generation spintronic devices based on their wide range of electronic and magnetic phases, which can be tuned by varying the host lattice or intercalant's identity, stoichiometry, or spatial order. Some of these compounds host a chiral magnetic phase in which the helical winding of magnetic moments propagates along a high-symmetry crystalline axis. Previous studies have demonstrated that variation in intercalant concentrations can have a dramatic effect on the formation of chiral domains and ensemble magnetic properties. However, a systematic and comprehensive study of how atomic-scale order and disorder impact these chiral magnetic textures is so far lacking. Here, we leverage a combination of imaging modes in the (scanning) transmission electron microscope (S/TEM) to directly probe (dis)order across multiple length scales and show how subtle changes in the atomic lattice can tune the mesoscale spin textures and bulk magnetic response in Cr1/3NbS2, with direct implications for the fundamental understanding and technological implementation of such compounds.

Development and Validation of a Prediction Model for Incident Hypothyroidism in a National Chronic Kidney Disease Cohort

CONTEXT

Hypothyroidism is a common yet under-recognized condition in patients with chronic kidney disease (CKD), which may lead to end-organ complications if left untreated.

OBJECTIVE

We developed a prediction tool to identify CKD patients at risk for incident hypothyroidism.

METHODS

Among 15 642 patients with stages 4 to 5 CKD without evidence of pre-existing thyroid disease, we developed and validated a risk prediction tool for the development of incident hypothyroidism (defined as thyrotropin [TSH] > 5.0 mIU/L) using the Optum Labs Data Warehouse, which contains de-identified administrative claims, including medical and pharmacy claims and enrollment records for commercial and Medicare Advantage enrollees as well as electronic health record data. Patients were divided into a two-thirds development set and a one-third validation set. Prediction models were developed using Cox models to estimate probability of incident hypothyroidism.

RESULTS

There were 1650 (11%) cases of incident hypothyroidism during a median follow-up of 3.4 years. Characteristics associated with hypothyroidism included older age, White race, higher body mass index, low serum albumin, higher baseline TSH, hypertension, congestive heart failure, exposure to iodinated contrast via angiogram or computed tomography scan, and amiodarone use. Model discrimination was good with similar C-statistics in the development and validation datasets: 0.77 (95% CI 0.75-0.78) and 0.76 (95% CI 0.74-0.78), respectively. Model goodness-of-fit tests showed adequate fit in the overall cohort (P = .47) as well as in a subcohort of patients with stage 5 CKD (P = .33).

CONCLUSION

In a national cohort of CKD patients, we developed a clinical prediction tool identifying those at risk for incident hypothyroidism to inform prioritized screening, monitoring, and treatment in this population.

Demystification and feasibility of CRISPR technology and gene editing in African laboratories

Clustered regularly interspaced short palindromic repeats, or CRISPR, is a powerful molecular biology tool that is enabling high-quality genetic research and engineering. However, for practical reasons, but more specifically because of the lack of training and the rapid development of gene-editing technology, the technique is still not well established in African laboratories. For this reason, a consortium formed by the Institut Pasteur of Tunis and Learn and Win decided to organise an international conference and workshop on CRISPR technology in particular and gene editing in general, focusing on the low-budget model more appropriate to the African context. From 12 to 17 June 2023, more than 200 interdisciplinary researchers and students from the life sciences and more than 20 international speakers and trainers gathered at the Institut Pasteur in Tunis, Tunisia, for the First African Conference and Workshop on CRISPR to discuss the latest gene editing technologies and discoveries. This Meeting Review describes the scientific event and highlights the main outcomes of both the conferences and the practical sessions. The symposium was a real success and thrives to educate, train and network international and young scientists in the field of gene editing and gene engineering.

Metabolite Stability in Archived Neonatal Dried Blood Spots Used for Epidemiologic Research

Epidemiologic studies of low-frequency exposures or outcomes using metabolomics analyses of neonatal dried blood spots (DBS) often require assembly of samples with substantial differences in duration of storage. Independent assessment of stability of metabolites in archived DBS will enable improved design and interpretation of epidemiologic research utilizing DBS. Neonatal DBS routinely collected and stored as part of the California Genetic Disease Screening Program between 1983 and 2011 were used. The study population included 899 children without cancer before age 6 years, born in California. High-resolution metabolomics with liquid-chromatography mass spectrometry was performed, and the relative ion intensities of common metabolites and selected xenobiotic metabolites of nicotine (cotinine and hydroxycotinine) were evaluated. In total, we detected 26,235 mass spectral features across 2 separate chromatography methods (C18 hydrophobic reversed-phase chromatography and hydrophilic-interaction liquid chromatography). For most of the 39 metabolites related to nutrition and health status, we found no statistically significant annual trends across the years of storage. Nicotine metabolites were captured in the DBS with relatively stable intensities. This study supports the usefulness of DBS stored long-term for epidemiologic studies of the metabolome. -Omics-based information gained from DBS may also provide a valuable tool for assessing prenatal environmental exposures in child health research.

Actin and CDC-42 contribute to nuclear migration through constricted spaces in C. elegans

Successful nuclear migration through constricted spaces between cells or in the extracellular matrix relies on the ability of the nucleus to deform. Little is known about how this takes place in vivo. We have studied confined nuclear migration in Caenorhabditis elegans larval P cells, which is mediated by the LINC complex to pull nuclei towards the minus ends of microtubules. Null mutations of the LINC component unc-84 lead to a temperature-dependent phenotype, suggesting a parallel pathway for P-cell nuclear migration. A forward genetic screen for enhancers of unc-84 identified cgef-1 (CDC-42 guanine nucleotide exchange factor). Knockdown of CDC-42 in the absence of the LINC complex led to a P-cell nuclear migration defect. Expression of constitutively active CDC-42 partially rescued nuclear migration in cgef-1; unc-84 double mutants, suggesting that CDC-42 functions downstream of CGEF-1. The Arp2/3 complex and non-muscle myosin II (NMY-2) were also found to function parallel to the LINC pathway. In our model, CGEF-1 activates CDC-42, which induces actin polymerization through the Arp2/3 complex to deform the nucleus during nuclear migration, and NMY-2 helps to push the nucleus through confined spaces.

Impact of SARS-CoV-2 Infection on the Association Between Laboratory Tests and Severe Outcomes Among Hospitalized Children

Background

To assist clinicians with identifying children at risk of severe outcomes, we assessed the association between laboratory findings and severe outcomes among severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected children and determined if SARS-CoV-2 test result status modified the associations.

Methods

We conducted a cross-sectional analysis of participants tested for SARS-CoV-2 infection in 41 pediatric emergency departments in 10 countries. Participants were hospitalized, had laboratory testing performed, and completed 14-day follow-up. The primary objective was to assess the associations between laboratory findings and severe outcomes. The secondary objective was to determine if the SARS-CoV-2 test result modified the associations.

Results

We included 1817 participants; 522 (28.7%) SARS-CoV-2 test-positive and 1295 (71.3%) test-negative. Seventy-five (14.4%) test-positive and 174 (13.4%) test-negative children experienced severe outcomes. In regression analysis, we found that among SARS-CoV-2-positive children, procalcitonin ≥0.5 ng/mL (adjusted odds ratio [aOR], 9.14; 95% CI, 2.90-28.80), ferritin >500 ng/mL (aOR, 7.95; 95% CI, 1.89-33.44), D-dimer ≥1500 ng/mL (aOR, 4.57; 95% CI, 1.12-18.68), serum glucose ≥120 mg/dL (aOR, 2.01; 95% CI, 1.06-3.81), lymphocyte count <1.0 × 109/L (aOR, 3.21; 95% CI, 1.34-7.69), and platelet count <150 × 109/L (aOR, 2.82; 95% CI, 1.31-6.07) were associated with severe outcomes. Evaluation of the interaction term revealed that a positive SARS-CoV-2 result increased the associations with severe outcomes for elevated procalcitonin, C-reactive protein (CRP), D-dimer, and for reduced lymphocyte and platelet counts.

Conclusions

Specific laboratory parameters are associated with severe outcomes in SARS-CoV-2-infected children, and elevated serum procalcitonin, CRP, and D-dimer and low absolute lymphocyte and platelet counts were more strongly associated with severe outcomes in children testing positive compared with those testing negative.

The determination of optimum segmentation parameters using genetic algorithms: Application to different segmentation algorithms and transmission electron microscopy tomography reconstructed volumes

A method for optimizing an automatic selection of values for parameters that feed segmentation algorithms is proposed. Evolutionary optimization techniques in combination with a fitness function based on a mutual information parameter have been used to find the optimal parameter values of region growing, fuzzy c-means and graph cut segmentation algorithms. To validate the method, the segmentation of two transmission electron microscopy tomography reconstructed volumes of a carbon black-reinforced rubber and a polylactic acid and clay nanocomposite is carried out (i) using evolutionary optimization techniques and (ii) manually by experts. The results confirm that the use of evolutionary optimization techniques, such as genetic algorithms, reduces the computational operation cost needed for a total grid search of segmentation parameters, reducing the probability of reaching a false optimum, and improving the segmentation quality. HIGHLIGHTS: A new approach to optimize 3D segmentation algorithms. Methodology to optimize segmentation parameters and improve segmentation quality. Improvement on the results when using region growing, fuzzy c-means and graph cuts algorithms.

Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis

Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.