Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing.

The sea cucumber (H. glaberrima) is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and functional profiles present in the sea cucumber, total DNA was obtained from their intestinal system, fosmid libraries constructed, and subsequent sequencing was performed. The diversity profile displayed that the most predominant domain was Bacteria (76.56 %), followed by Viruses (23.24 %) and Archaea (0.04 %). Within the 11 phyla identified, the most abundant was Proteobacteria (73.16 %), followed by Terrabacteria group (3.20 %) and Fibrobacterota, Chlorobiota, Bacteroidota (FCB) superphylum (1.02 %). The most abundant species were Porvidencia rettgeri (21.77 %), Pseudomonas stutzeri (14.78 %), and Alcaligenes faecalis (5.00 %). The functional profile revealed that the most abundant functions are related to transporters, MISC (miscellaneous information systems), organic nitrogen, energy, and carbon utilization. The data collected in this project on the diversity and functional profiles of the intestinal system of the H. glaberrima provided a detailed view of its microbial ecology. These findings may motivate comparative studies aimed at understanding the role of the microbiome in intestinal regeneration.

Effect of Christmas Holidays on Type 1 Diabetes Mellitus in Users of Glucose Flash Systems.

OBJECTIVE: Christmas holidays can impact weight and glycemic control in type 2 diabetes, but their effect on type 1 diabetes (T1D) remains understudied. This study assessed how Christmas holidays affect individuals with T1D who use flash continuous glucose monitoring systems. METHODS: This retrospective study involved 812 adults diagnosed with T1D recruited from 3 hospitals. Clinical, anthropometric, and socioeconomic data were collected. Glucose metrics from 14 days before January 1st, and before December 1st and February 1st as control periods, were recorded. Analyses adjusted for multiple variables were conducted to assess the holiday season's impact on glycemic control. RESULTS: The average time in range during the holidays (60.0 ± 17.2%) was lower compared to December (61.9 ± 17.2%, P < .001) and February (61.7 ± 17.7%, P < .001). Time above range (TAR > 180 mg/dL) was higher during Christmas (35.8 ± 18.2%) compared to December (34.1 ± 18.3%, P < .001) and February (34.2 ± 18.4%, P < .001). Differences were also observed in TAR >250 mg/dL, coefficient of variation, and average glucose (P < .05). No differences were found in time below range or other metrics. Linear regression models showed that the holidays reduced time in range by 1.9% (ß = -1.92, P = .005) and increased TAR >180 mg/dL by 1.8% (ß = 1.75, P = .016). CONCLUSION: Christmas holidays are associated with a mild and reversible deterioration in glucose metrics among individuals with T1D using flash continuous glucose monitoring, irrespective of additional influencing factors. These discoveries can be useful to advise individuals with diabetes during the festive season and to recognize potential biases within studies conducted during this timeframe.

iSCORE-PD: an isogenic stem cell collection to research Parkinson's Disease.

Parkinson's disease (PD) is a neurodegenerative disorder caused by complex genetic and environmental factors. Genome-edited human pluripotent stem cells (hPSCs) offer the uniique potential to advance our understanding of PD etiology by providing disease-relevant cell-types carrying patient mutations along with isogenic control cells. To facilitate this experimental approach, we generated a collection of 55 cell lines genetically engineered to harbor mutations in genes associated with monogenic PD (SNCA A53T, SNCA A30P, PRKN Ex3del, PINK1 Q129X, DJ1/PARK7 Ex1-5del, LRRK2 G2019S, ATP13A2 FS, FBXO7 R498X/FS, DNAJC6 c.801 A>G+FS, SYNJ1 R258Q/FS, VPS13C A444P, VPS13C W395C, GBA1 IVS2+1). All mutations were generated in a fully characterized and sequenced female human embryonic stem cell (hESC) line (WIBR3; NIH approval number NIHhESC-10-0079) using CRISPR/Cas9 or prime editing-based approaches. We implemented rigorous quality controls, including high density genotyping to detect structural variants and confirm the genomic integrity of each cell line. This systematic approach ensures the high quality of our stem cell collection, highlights differences between conventional CRISPR/Cas9 and prime editing and provides a roadmap for how to generate gene-edited hPSCs collections at scale in an academic setting. We expect that our isogenic stem cell collection will become an accessible platform for the study of PD, which can be used by investigators to understand the molecular pathophysiology of PD in a human cellular setting.

Impact of socioeconomic status on chronic control and complications of type 1 diabetes mellitus in users of glucose flash systems: a follow-up study.

BACKGROUND: This study investigates the association between socioeconomic status (SES) and glycemic control in individuals with type 1 diabetes (T1D) using flash glucose monitoring (FGM) devices within a public health system where these technologies are freely available and utilized according to recommended guidelines. METHODS: A follow-up study of 1060 adults (mean age 47.4 ± 15.0 years, 49.0% women) with T1D, receiving care at three Spanish university hospitals that regularly employ the FGM system. SES was assessed using the Spanish Deprivation Index and the average annual net income per person. Glycemic data were collected over a 14-day follow-up period, including baseline glycated hemoglobin (HbA1c) levels prior to sensor placement, the last available HbA1c levels, and FGM-derived glucose metrics. Individuals with sensor usage time < 70% were excluded. Chronic micro and macrovascular complications related to diabetes were documented. Regression models, adjusted for clinical variables, were employed to determine the impact of SES on optimal sensor control (defined as time in range (TIR) ≥ 70% with time below range < 4%) and disease complications. RESULTS: The average follow-up was of 2 years. The mean TIR and the percentage of individuals with optimal control were higher in individuals in the highest SES quartile (64.9% ± 17.8% and 27.9%, respectively) compared to those in the lowest SES quartile (57.8 ± 17.4% and 12.1%) (p < 0.001). Regression models showed a higher risk of suboptimal control (OR 2.27, p < 0.001) and ischemic heart disease and/or stroke (OR 3.59, p = 0.005) in the lowest SES quartile. No association was observed between SES and the risk of diabetic nephropathy and retinopathy. FGM system improved HbA1c levels across all SES quartiles. Although individuals in the highest SES quartile still achieved a significantly lower value at the end of the follow-up 55 mmol/mol (7.2%) compared to those in the lowest SES quartile 60 mmol/mol (7.6%) (p < 0.001), the significant disparities in this parameter between the various SES groups were significantly reduced after FGM technology use. CONCLUSIONS: Socioeconomic status plays a significant role in glycemic control and complications in individuals with T1D, extending beyond access to technology and its proper utilization. The free utilization of FGM technology helps alleviate the impact of social inequalities on glycemic control.

Scans per day as predictors of optimal glycemic control in people with type 1 diabetes mellitus using flash glucose monitoring: what number of scans per day should raise a red flag?

AIMS: This study aimed to determine the minimum frequency of flash glucose monitoring (FGM) scans necessary for optimal glycemic control in patients with type 1 diabetes (T1D). METHODS: Data were collected from 692 patients (47.5% female, with a median age of 47.4 years) who used FGM systems daily and recorded their clinical variables and device data. RESULTS: Logistic regression models showed that performing more than 12 scans per day was associated with improved T1D control (OR = 4.22, p < 0.001) and a reduction in HbA1c (7.6 vs 7.0%, 60-53 mmol/mol p < 0.001). However, those performing less than 6 scans showed no improvement in HbA1c (7.9 vs 7.8%, 63-61 mmol/mol p = 0.514). Thirteen daily scans were determined as the optimal cutoff point for predicting optimal glycemic control using a maximally selected rank algorithm. Significant reductions were observed in mean glucose (< 0.001), coefficient of variation (< 0.001), HbA1c (< 0.001), and an increase in TIR (< 0.001) in patients who performed more than 12 daily scans. CONCLUSIONS: The results suggest that a higher frequency of daily scans by T1D patients using FGM systems leads to improved chronic glycemic control. The minimum recommended frequency for optimal control is 13 scans per day, and more than 6 daily scans are needed to improve HbA1c.

Polymer Implantable Electrode Foundry: A shared resource for manufacturing polymer-based microelectrodes for neural interfaces.

Large scale monitoring of neural activity at the single unit level can be achieved via electrophysiological recording using implanted microelectrodes. While neuroscience researchers have widely employed chronically implanted electrode-based interfaces for this purpose, a commonly encountered limitation is loss of highly resolved signals arising from immunological response over time. Next generation electrode-based interfaces improve longitudinal signal quality using the strategy of stabilizing the device-tissue interface with microelectrode arrays constructed from soft and flexible polymer materials. The limited availability of such polymer microelectrode arrays has restricted access to a small number of researchers able to build their own custom devices or who have developed specific collaborations with engineering researchers who can produce them. Here, a new technology resource model is introduced that seeks to widely increase access to polymer microelectrode arrays by the neuroscience research community. The Polymer Implantable Electrode (PIE) Foundry provides custom and standardized polymer microelectrode arrays as well as training and guidance on best-practices for implantation and chronic experiments.

Domestication shapes the pig gut microbiome and immune traits from the scale of lineage to population.

Animal ecology and evolution have long been known to shape host physiology, but more recently, the gut microbiome has been identified as a mediator between animal ecology and evolution and health. The gut microbiome has been shown to differ between wild and domestic animals, but the role of these differences for domestic animal evolution remains unknown. Gut microbiome responses to new animal genotypes and local environmental change during domestication may promote specific host phenotypes that are adaptive (or not) to the domestic environment. Because the gut microbiome supports host immune function, understanding the effects of animal ecology and evolution on the gut microbiome and immune phenotypes is critical. We investigated how domestication affects the gut microbiome and host immune state in multiple pig populations across five domestication contexts representing domestication status and current living conditions: free-ranging wild, captive wild, free-ranging domestic, captive domestic in research or industrial settings. We observed that domestication context explained much of the variation in gut microbiome composition, pathogen abundances and immune markers, yet the main differences in the repertoire of metabolic genes found in the gut microbiome were between the wild and domestic genetic lineages. We also documented population-level effects within domestication contexts, demonstrating that fine scale environmental variation also shaped host and microbe features. Our findings highlight that understanding which gut microbiome and immune traits respond to host genetic lineage and/or scales of local ecology could inform targeted interventions that manipulate the gut microbiome to achieve beneficial health outcomes.

QSAR analysis of five generations of cephalosporins to establish the structural basis of activity against methicillin-resistant and methicillin-sensitive Staphylococcus aureus.

Solving the worldwide problem of growing bacterial drug resistance will require a short-run and medium-term strategy. Structure-activity relationship (SAR) and quantitative SAR (QSAR) analyses have recently been utilized to reveal the molecular basis of the antibacterial activity and antibacterial spectrum of penicillins, the use of which is no longer solely empirical. Likewise, a more rational drug design can be achieved with cephalosporins, the largest group of ß-lactam antibiotics. The current contribution aimed to establish the molecular and physicochemical basis of the antibacterial activity of five generations of cephalosporins on methicillin-sensitive (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA). With SAR and QSAR analyses, the molecular portions that provide essential and additional antibacterial activity were identified. The substitutions with greater volume and polarity on the R2 side chain of the cephem nucleus increase potency on MSSA. The best effect is produced by substitutions with polar nitrogen atoms at the alpha-carbon (Cα). Substitutions with greater volume and polarity on the R1 side chain further enhance antibacterial activity. In contrast, the effect against MRSA seems to be independent of any substitution on R2 or at the Cα, while depending on the accessory portions with greater volume and polarity on R1.

Continuous Glucose Monitoring as an Additional Tool in Early Cystic Fibrosis-Related Diabetes Monitoring and in Evaluation of Short-Term Sitagliptin Response.

Cystic fibrosis-related diabetes (CFRD) is a complication associated with a negative prognosis in patients with cystic fibrosis (CF). Although the oral glucose tolerance test (OGTT) is the widely recommended screening test for CFRD diagnosis, continuous glucose monitoring (CGM) is increasingly considered a useful and easy-to-perform test for diagnosis and follow-up in clinical practice. Regarding CFRD treatment, although insulin is the classic approved pharmacological option, incretins could also be a helpful alternative in early stages. CGM could be also a useful tool to measure the early response to this therapy. METHODS: We studied 25 CF patients with abnormal OGTT results and compared glucose and insulin levels during the OGTTs with CGM results as a tool for early CFRD diagnosis. In addition, we evaluated glycaemic control with CGM before and after treatment with sitagliptin. RESULTS: A correlation was found between lower plasma insulin levels during the OGTTs and higher average sensor glucose (p = 0.009) and hyperglycaemic excursions (p = 0.017). The CGM data on sitagliptin treatment (n = 25) showed an average glycaemic improvement from 124.2 to 117.2 mg/dL (p = 0.002) with a 5.6-point standard deviation of glucose decrease (p < 0.001). Hyperglycaemic excursions ≥200 mg/dL diminished 57.1% (p = 0.021). Both time in range and time above 180 mg/dL improved during treatment (p = 0.036 and p = 0.006, respectively). CONCLUSION: CGM is a useful tool that offers valuable information for both the diagnosis and the management of CFRD. Lower plasma insulin levels during OGTTs are associated with a poor ambulatory glucose profile in CGM. Sitagliptin could play an important role in the treatment of the early stages of CFRD.

Tonic TNF conditioning of macrophages safeguards stimulus-specific inflammatory responses.

Tumor necrosis factor (TNF) is a key inflammatory cytokine that warns recipient cells of a nearby infection or tissue damage. Acute exposure to TNF activates characteristic oscillatory dynamics of the transcription factor NFκB and induces a characteristic gene expression program; these are distinct from the responses of cells directly exposed to pathogen-associated molecular patterns (PAMPs). Here, we report that tonic TNF exposure is critical for safeguarding TNF's specific functions. In the absence of tonic TNF conditioning, acute exposure to TNF causes (i) NFκB signaling dynamics that are less oscillatory and more like PAMP-responsive NFκB dynamics, (ii) immune gene expression that is more similar to the Pam3CSK4 response program, and (iii) broader epigenomic reprogramming that is characteristic of PAMP-responsive changes. We show that the absence of tonic TNF signaling effects subtle changes to TNF receptor availability and dynamics such that enhanced pathway activity results in non-oscillatory NFκB. Our results reveal tonic TNF as a key tissue determinant of the specific cellular responses to acute paracrine TNF exposure, and their distinction from responses to direct exposure to PAMPs.

Captive and urban environments are associated with distinct gut microbiota in deer mice (Peromyscus maniculatus).

Animals in captive and urban environments encounter evolutionarily novel conditions shaped by humans, such as altered diets, exposure to human-associated bacteria, and, potentially, medical interventions. Captive and urban environments have been demonstrated to affect gut microbial composition and diversity independently but have not yet been studied together. By sequencing the gut microbiota of deer mice living in laboratory, zoo, urban and natural settings, we sought to identify (i) whether captive deer mouse gut microbiota have similar composition regardless of husbandry conditions and (ii) whether captive and urban deer mice have similar gut microbial composition. We found that the gut microbiota of captive deer mice were distinct from those of free-living deer mice, indicating captivity has a consistent effect on the deer mouse microbiota regardless of location, lineage or husbandry conditions for a population. Additionally, the gut microbial composition, diversity and bacterial load of free-living urban mice were distinct from those of all other environment types. Together, these results indicate that gut microbiota associated with captivity and urbanization are likely not a shared response to increased exposure to humans but rather are shaped by environmental features intrinsic to captive and urban conditions.

New and Repurposed Drugs for the Treatment of Active Tuberculosis: An Update for Clinicians.

Although tuberculosis (TB) is preventable and curable, the lengthy treatment (generally 6 months), poor patient adherence, high inter-individual variability in pharmacokinetics (PK), emergence of drug resistance, presence of comorbidities, and adverse drug reactions complicate TB therapy and drive the need for new drugs and/or regimens. Hence, new compounds are being developed, available drugs are repurposed, and the dosing of existing drugs is optimized, resulting in the largest drug development portfolio in TB history. This review highlights a selection of clinically available drug candidates that could be part of future TB regimens, including bedaquiline, delamanid, pretomanid, linezolid, clofazimine, optimized (high dose) rifampicin, rifapentine, and para-aminosalicylic acid. The review covers drug development history, preclinical data, PK, and current clinical development.

A prospective study to assess the impact of a novel CFTR therapy combination on body composition in patients with cystic fibrosis with F508del mutation.

BACKGROUND & AIM: Malnutrition is a prevalent condition in Cystic Fibrosis (CF) and can result in worsening of pulmonary function and other comorbidities. Cystic fibrosis transmembrane regulator (CFTR) modulator therapies are improving the CF-related care and outcomes. Body Mass Index (BMI) is the most commonly used parameter to assess nutritional status, albeit it is a very unspecific indicator. Hence, current guidelines recommend body composition analysis as a part of nutritional assessment. The aim of our study was to evaluate the impact of elexacaftor-tezacaftor-ivacaftor (ELX/TEZ/IVA) treatment on body composition and respiratory function. METHODS: We recruited patients with CF from University Hospital La Princesa, with follow-up in the Adult Cystic Fibrosis Unit. All patients were eligible to initiate ELX/TEZ/IVA therapy. Body composition was assessed with a Bioelectrical Impedance Analysis (BIA) and spirometry data were obtained before and after 6 months of treatment. RESULTS: Our study sample was composed of 36 patients with CF. We observed a significant increase in BMI after 6 months of treatment (p < 0.001), as well as an increase in fat mass (p = 0.008) and visceral fat area (p = 0.026). The other body composition parameters did not yield significant changes. Overall, %FEV1 increased from 72.67 % (±17.39) to 84.74 % (±18.18) after 6 months of treatment. Interestingly, we found an inverse correlation between %FEV1 and fat mass (r = -0,476; p = 0,0058), %FEV1 and age (r = -0,411; p = 0,0196) and between %FEV1 and visceral fat area (r = -0,515; p = 0,0025). On the contrary, we found a direct correlation between %FEV1 and body cell mass (r = 0,367; p = 0,038). CONCLUSIONS: Novel CFTR modulators are emerging for the treatment of CF. Specifically, triple combination with ELX/TEZ/IVA has shown to effectively improve both pulmonary and nutritional status in patients with CF with F508del mutation. Body composition should be a part of the routine assessment for patients with CF.

Go for the gold: Hurdles and winning strategies for conducting longitudinal and nonlinear research in undergraduate leader development.

This article makes a case for longitudinal and non-linear methods when researching or evaluating student leadership development. After a primer on longitudinal methodology, barriers and aligned solutions to methodological challenges are presented.

Acute in vivo Recording with a Generic Parylene Microelectrode Array Implanted with Dip-coating Method into the Rat Brain.

Flexible polymer-based microelectrode arrays (MEAs) can reduce tissue inflammation and foreign body response and greatly prolong the lifetime of neural implants. However, standard and customized polymer devices are only accessible to limited groups. To better promote the development and application of polymer MEAs, we have launched the Polymer Implantable Electrode (PIE) Foundry and developed a 64-channel Parylene C-based MEA with generic electrodes layout that can be used to record from both cortical and sub-cortical regions in rodents. In addition, a practical dip-coating protocol for the insertion of the flexible standard Parylene MEA is developed.

Exceptional larval morphology of nine species of the Anastrephamucronota species group (Diptera, Tephritidae).

Anastrepha is the most diverse and economically important genus of Tephritidae in the American tropics and subtropics. The striking morphology of the third instars of Anastrephacaballeroi Norrbom, Anastrephacrebra Stone, Anastrephahaplacantha Norrbom & Korytkowski, Anastrephakorytkowskii Norrbom, Anastrephanolazcoae Norrbom & Korytkowski, and three newly discovered and as yet formally unnamed species (Anastrepha sp. Peru-82, Anastrephasp.nr.protuberans, and Anastrepha sp. Sur-16), and the more typical morphology of Anastrephaaphelocentema Stone, are described using light and scanning electron microscopy. To contribute to a better understanding of the interspecific and intraspecific variation among species in the mucronota species group and facilitate phylogenetic studies, we integrate molecular and morphological techniques to confirm the identity and describe third instars. Larva-adult associations and the identification of described larvae were confirmed using DNA barcodes. We provide diagnostic characters to distinguish larvae among these nine species of the mucronota group and separate them from those of the 29 other Anastrepha species previously described. We introduce the vertical comb-like processes on the oral margin as a novel character, and the unusual character states, including position and shape of the preoral lobe, and dentate or fringed posterior margins of the oral ridges and accessory plates. Our comparative morphology concurs with most previously inferred phylogenetic relationships within the mucronota group.

Possibilities and limits for using the gut microbiome to improve captive animal health.

Because of its potential to modulate host health, the gut microbiome of captive animals has become an increasingly important area of research. In this paper, we review the current literature comparing the gut microbiomes of wild and captive animals, as well as experiments tracking the microbiome when animals are moved between wild and captive environments. As a whole, these studies report highly idiosyncratic results with significant differences in the effect of captivity on the gut microbiome between host species. While a few studies have analyzed the functional capacity of captive microbiomes, there has been little research directly addressing the health consequences of captive microbiomes. Therefore, the current body of literature cannot broadly answer what costs, if any, arise from having a captive microbiome in captivity. Addressing this outstanding question will be critical to determining whether it is worth pursuing microbial manipulations as a conservation tool. To stimulate the next wave of research which can tie the captive microbiome to functional and health impacts, we outline a wide range of tools that can be used to manipulate the microbiome in captivity and suggest a variety of methods for measuring the impact of such manipulation preceding therapeutic use. Altogether, we caution researchers against generalizing results between host species given the variability in gut community responses to captivity and highlight the need to understand what role the gut microbiome plays in captive animal health before putting microbiome manipulations broadly into practice.

Subacute Thyroiditis and Heart Failure in a Patient Presenting With COVID-19.

A 67-year-old male was admitted with shortness of breath and diarrhea. His COVID-19 polymerase chain reaction test was positive, and he was found to be in acute heart failure. Troponin levels were elevated, echocardiogram showed ejection fraction of 24%, and his electrocardiogram was normal. Inflammatory markers were elevated. Further testing revealed suppressed thyroid-stimulating hormone and elevated free thyroxine (T4). Differential diagnosis at this point included possible myocarditis from the viral illness, exacerbation of heart failure from the viral infection or from thyrotoxicosis was considered. Patient's heart failure improved with initiation of heart failure therapies; however, biochemically, his thyroid function tests (TFTs) did not improve, despite empiric methimazole. Thyroid antibody tests were unremarkable. Thyroid ultrasound showed mildly enlarged thyroid gland with no increased vascularity and 5-mm bilateral cysts. Thyroid dysfunction was attributed to subacute thyroiditis from COVID-19, methimazole was tapered, and prednisone was initiated. The patient's TFTs improved. With the ongoing COVID-19 pandemic, it is imperative that clinicians keep a broad differential in individuals presenting with heart failure, and obtaining baseline TFTs may be reasonable. Rapid treatment of the underlying thyroiditis is important in these patients to improve the cardiovascular outcomes. In our experience, steroid therapy showed a rapid improvement in the TFTs.