Metabolism at the crossroads of inflammation and fibrosis in chronic kidney disease.

Chronic kidney disease (CKD), defined as persistent (>3 months) kidney functional loss, has a growing prevalence (>10% worldwide population) and limited treatment options. Fibrosis driven by the aberrant accumulation of extracellular matrix is the final common pathway of nearly all types of chronic repetitive injury in the kidney and is considered a hallmark of CKD. Myofibroblasts are key extracellular matrix-producing cells that are activated by crosstalk between damaged tubules and immune cells. Emerging evidence indicates that metabolic alterations are crucial contributors to the pathogenesis of kidney fibrosis by affecting cellular bioenergetics and metabolite signalling. Immune cell functions are intricately connected to their metabolic characteristics, and kidney cells seem to undergo cell-type-specific metabolic shifts in response to damage, all of which can determine injury and repair responses in CKD. A detailed understanding of the heterogeneity in metabolic reprogramming of different kidney cellular subsets is essential to elucidating communication processes between cell types and to enabling the development of metabolism-based innovative therapeutic strategies against CKD.

Disulfide Tethering to Map Small Molecule Binding Sites Transcriptome-wide.

We report the development of Tether-seq, a transcriptome-wide screen to probe RNA-small molecule interactions using disulfide tethering. This technique uses s4U metabolic labeling to provide sites for reversible and covalent attachment of small molecule disulfides to the transcriptome. By screening under reducing conditions, we identify interactions that are stabilized by binding over those driven by the reactivity of the RNA sites. When applied to cellular RNA, Tether-seq with a disulfide analogue of risdiplam, an FDA-approved drug that targets RNA to treat spinal muscular atrophy (SMA), revealed a number of potential binding sites, most prominently at a site within the cytochrome C oxidase 1 (COX1) transcript. Structure probing by SHAPE-MaP revealed a structured motif and confirmed binding to the lead molecule. This work demonstrates that these screens have the power to identify binding sites throughout the transcriptome and provide invaluable insight into the thermodynamic properties that define small molecule binding.

Clinical Implications of Over- and Under-Triage Using Need for Trauma Intervention and Cribari Indices.

BACKGROUND: Need for Trauma Intervention (NFTI) score was proposed to help identify injured trauma patients while minimizing under (UT) and over triage (OT). Using a national database, we aimed to describe UT and OT of NFTI vs standard Cribari method (CM) and hypothesized triage sensitivity remains poor. METHODS: The 2021 Trauma Quality Improvement Program (TQIP) database was queried. Demographics, mechanism, verification level, interfacility transfer (IF), and level of activation were collected. Patients were stratified by both NFTI [+ vs -] and CM [Injury severity score (ISS) < 15 vs > 15]. UT was defined as NFTI + or ISS >15 without full trauma activation. RESULTS: 1,030,526 patients were identified in TQIP. 84,969 were UT and 97,262 were OT using NFTI while 94,020 were UT and 108,823 were OT using CM. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of NFTI is 49%, 89%, 45%, and 90%, respectively vs 43%, 87%, 39%, and 89% of CM, respectively. Age was higher in the UT group using both scores (52 vs 42, P < .0001 and 54 vs 42, P < .0001, respectively). Using MLR, level 2 and 3 verification, blunt mechanism, female, IF, and older age were associated with UT in both NFTI and CM. Level 1 verification, penetrating mechanism, male, no IF, and younger age were associated with OT. CONCLUSIONS: Current prehospital triage criteria have poor sensitivity for identifying severely injured trauma patients by both NFTI and CM. UT increases as age of the patient increases. Further studies are needed to improve triage.

α-Synuclein triggers cofilin pathology and dendritic spine impairment via a PrPC-CCR5 dependent pathway.

Cognitive dysfunction and dementia are critical symptoms of Lewy Body dementias (LBD). Specifically, alpha-synuclein (αSyn) accumulation in the hippocampus leading to synaptic dysfunction is linked to cognitive deficits in LBD. Here, we investigated the pathological impact of αSyn on hippocampal neurons. We report that either αSyn overexpression or αSyn pre-formed fibrils (PFFs) treatment triggers the formation of cofilin-actin rods, synapse disruptors, in cultured hippocampal neurons and in the hippocampus of synucleinopathy mouse models and of LBD patients. In vivo, cofilin pathology is present concomitantly with synaptic impairment and cognitive dysfunction. Rods generation prompted by αSyn involves the co-action of the cellular prion protein (PrPC) and the chemokine receptor 5 (CCR5). Importantly, we show that CCR5 inhibition, with a clinically relevant peptide antagonist, reverts dendritic spine impairment promoted by αSyn. Collectively, we detail the cellular and molecular mechanism through which αSyn disrupts hippocampal synaptic structure and we identify CCR5 as a novel therapeutic target to prevent synaptic impairment and cognitive dysfunction in LBD.

RNA Sequencing Demonstrates Ex Vivo Neocortical Transcriptomic Changes Induced by Epileptiform Activity in Male and Female Mice.

Seizures are generally associated with epilepsy but may also be a symptom of many other neurological conditions. A hallmark of a seizure is the intensity of the local neuronal activation, which can drive large-scale gene transcription changes. Such changes in the transcriptional profile likely alter neuronal function, thereby contributing to the pathological process. Therefore, there is a strong clinical imperative to characterize how gene expression is changed by seizure activity. To this end, we developed a simplified ex vivo technique for studying seizure-induced transcriptional changes. We compared the RNA sequencing profile in mouse neocortical tissue with up to 3 h of epileptiform activity induced by 4-aminopyridine (4AP) relative to control brain slices not exposed to the drug. We identified over 100 genes with significantly altered expression after 4AP treatment, including multiple genes involved in MAPK, TNF, and neuroinflammatory signaling pathways, all of which have been linked to epilepsy previously. Notably, the patterns in male and female brain slices were almost identical. Various immediate early genes were among those showing the largest upregulation. The set of down-regulated genes included ones that might be expected either to increase or to decrease neuronal excitability. In summary, we found the seizure-induced transcriptional profile complex, but the changes aligned well with an analysis of published epilepsy-associated genes. We discuss how simple models may provide new angles for investigating seizure-induced transcriptional changes.

O blood type is not associated with worse coagulopathy or outcome in exsanguinating trauma.

BACKGROUND: Despite improving understanding of trauma-induced coagulopathy (TIC), mortality and morbidity due to exsanguinating trauma remain high. Increased complications due to hemorrhage have been reported in blood group O, possibly due to reduced levels of von Willebrand factor (vWF). METHODS: An urban level 1 adult trauma center registry was retrospectively queried. Patients receiving ≥6 units of pRBC within 4 â€‹h of presentation were included. Patient demographics, admission labs and outcomes were obtained. Univariate and multiple logistic regression analyses were performed. RESULTS: 562 patients were identified. There were no significant differences in demographics, admission labs, or outcome between different ABO groups. After adjustment, Type A patients were more likely to be hypocoagulable compared to Type O patients (p â€‹= â€‹0.014). No mortality differences were seen between ABO types in multiple regression analysis. CONCLUSIONS: No outcome or mortality differences were seen between ABO types, therefore factors other than vWF expression should be considered to explain coagulopathy in trauma patients.

Dietary acrylamide-linked burden of cancers in four sub-sahara African countries: A review and data synthesis.

Acrylamide (AA) is a food processing byproduct that forms at high temperatures and is classified as a probable human carcinogen. Previous studies have linked AA to kidney, uterus, and ovary cancer burdens, but its study in African countries remains underexplored. This study systematically used six recent articles on dietary AA concentration data from scholarly databases using specific search terms. We also collected health metrics secondary data from the Institute of Health Metrics and Evaluation and other sources for the period 2015-2019. We used a Monte-Carlo simulation to integrate the dietary AA exposure, risks, and health metrics to estimate the cancer burdens. The results showed that the modal healthy life years lost ranged from 0.00488 (Ghana) to 0.218 (Ethiopia) per 100,000 population. The median statistic indicated 1.2 and 26.10 healthy life years lost for Ghana and Ethiopia, respectively, due to the three cancer types. The four-country study areas' total disability-adjusted life years (DALYs) were 63.7 healthy life-year losses. Despite the limitations of the non-standardized age-related food consumption data and the few inclusive articles, the probabilistic approach may account for the uncertainties and provide valid conclusions.

Plasticity and not adaptation is the primary source of temperature-mediated variation in flowering phenology in North America.

Phenology varies widely over space and time because of its sensitivity to climate. However, whether phenological variation is primarily generated by rapid organismal responses (plasticity) or local adaptation remains unresolved. Here we used 1,038,027 herbarium specimens representing 1,605 species from the continental United States to measure flowering-time sensitivity to temperature over time (Stime) and space (Sspace). By comparing these estimates, we inferred how adaptation and plasticity historically influenced phenology along temperature gradients and how their contributions vary among species with different phenology and native climates and among ecoregions differing in species composition. Parameters Sspace and Stime were positively correlated (r = 0.87), of similar magnitude and more frequently consistent with plasticity than adaptation. Apparent plasticity and adaptation generated earlier flowering in spring, limited responsiveness in late summer and delayed flowering in autumn in response to temperature increases. Nonetheless, ecoregions differed in the relative contributions of adaptation and plasticity, from consistently greater importance of plasticity (for example, southeastern United States plains) to their nearly equal importance throughout the season (for example, Western Sierra Madre Piedmont). Our results support the hypothesis that plasticity is the primary driver of flowering-time variation along temperature gradients, with local adaptation having a widespread but comparatively limited role.

Vascular Endothelial Growth Factor-C Treatment Enhances Cerebrospinal Fluid Outflow during Toxoplasma gondii Brain Infection but Does Not Improve Cerebral Edema.

Cerebral edema frequently develops in the setting of brain infection and can contribute to elevated intracranial pressure, a medical emergency. How excess fluid is cleared from the brain is not well understood. Previous studies have shown that interstitial fluid is transported out of the brain along perivascular channels that collect into the cerebrospinal fluid (CSF)-filled subarachnoid space. CSF is then removed from the central nervous system through venous and lymphatic routes. The current study tested the hypothesis that increasing lymphatic drainage of CSF would promote clearance of cerebral edema fluid during infection with the neurotropic parasite Toxoplasma gondii. Fluorescent microscopy and magnetic resonance imaging was used to show that C57BL/6 mice develop vasogenic edema 4 to 5 weeks after infection with T. gondii. Tracer experiments were used to evaluate how brain infection affects meningeal lymphatic function, which demonstrated a decreased rate in CSF outflow in T. gondii-infected mice. Next, mice were treated with a vascular endothelial growth factor (VEGF)-C-expressing viral vector, which induced meningeal lymphangiogenesis and improved CSF outflow in chronically infected mice. No difference in cerebral edema was observed between mice that received VEGF-C and those that rececived sham treatment. Therefore, although VEGF-C treatment can improve lymphatic outflow in mice infected with T. gondii, this effect does not lead to increased clearance of edema fluid from the brains of these mice.

Key Findings on Computed Tomography of the Head that Predict Death or the Need for Neurosurgical Intervention From Traumatic Brain Injury.

BACKGROUND: Traumatic brain injury (TBI) requires rapid management to avoid secondary injury or death. This study evaluated if a simple schema for quickly interpreting CT head (CTH) imaging by trauma surgeons and trainees could be validated to predict need for neurosurgical intervention (NSI) or death from TBI within 24 hours. METHODS: We retrospectively reviewed TBI patients presenting to our trauma center in 2020 with blunt mechanism and GCS ≤ 12. Primary independent variables were presence of 7 normal findings on CTH (CSF at foramen magnum, open fourth ventricle, CSF around quadrigeminal plate, CSF around cerebral peduncles, absence of midline shift, visible sulci/gyri, and gray-white differentiation). Trauma surgeons and trainees separately evaluated each patient's CTH, scoring findings as normal or abnormal. Primary outcome was NSI/death in 24 hours. RESULTS: Our population consisted of 444 patients; 21.4% received NSI or died within 24 hours. By trainees' interpretation, 5.8% of patients without abnormal findings had NSI/death vs 52.0% of patients with ≥1 abnormality; attending interpretation was 8.7% and 54.9%, respectively (P < .001). Sulci/gyri effacement, midline shift, and cerebral peduncle effacement maximized sensitivity and specificity for predicting NSI/death. Considering pooled results, when ≥1 of those 3 findings was abnormal, sensitivity was 77.89%, specificity was 80.80%, positive predictive value was 52.48%, and negative predictive value was 93.07%. DISCUSSION: Any single abnormality in this schema significantly predicted a large increase in NSI/death in 24 hours in TBI patients, and three particular findings were most predictive. This schema may help predict need for intervention and expedite management of moderate/severe TBI.

Trust but Verify? Utility of Intraoperative Angiography After Revascularization for Vascular Trauma.

BACKGROUND: Trauma surgical dogma teaches that patients should have intraoperative angiography (IA) if the surgeon cannot identify a pulse in the injured extremity following a vascular repair. This study was undertaken to assess the utility of IA in trauma patients who underwent open brachial or femoral artery revascularization. METHODS: Retrospective analysis of the Prospective Observational Vascular Injury Trial (PROOVIT) database from 2013 to 2021 evaluated patients >15 years with penetrating or blunt injuries requiring operative intervention of the brachial, superficial femoral, or common femoral arteries. Prospective Observational Vascular Injury Trial data evaluated included documented pulse in the injured extremity at revascularization completion, adjunctive IA, immediate revision, and vascular reintervention during the hospitalization. RESULTS: Of the 5057 patients with vascular injury, 185 patients met our inclusion criteria. The majority were male (86.5%) with a median age, injury severity score, and systolic blood pressure of 29, 12, and 117, respectively. Of the study patients, 39% underwent IA, 14% had immediate revision, and 8% required vascular reoperation during their admission. Patients who underwent IA and with no documented palpable pulse after repair were significantly more likely to require immediate revision before leaving the operating room (22% vs 9%, P = .013) and were not more likely to require reoperation, than those who did not undergo IA (7% vs 9%, P = .613). CONCLUSIONS: Intraoperative angiography is a valuable tool for surgeons for vascular extremity trauma and is associated with a greater rate of immediate revision. Familiarity with angiographic technique is essential for vascular trauma and should be a focal point of training.

Synchronous tracheostomy and gastrostomy placement results in shorter length of stay in traumatic brain injury patients.

BACKGROUND: American Society for Parenteral and Enteral Nutrition (ASPEN) guidelines recommend gastrostomy for patients suspected to require enteral access device for 4-6 weeks. Our hypothesis was that traumatic brain injury (TBI) patients undergoing synchronous tracheostomy/gastrostomy (SYNC) compared to tracheostomy first (DELAY) have shorter length of stay (LOS) but higher rates of unnecessary gastrostomy. METHODS: Retrospective review of TBI patients requiring tracheostomy in 2017-2022 â€‹at a Level 1 trauma center was conducted. SYNC and DELAY patients were compared, and CoxPH analysis was performed for LOS. RESULTS: 394 patients were included [mean age: 42 (SD:18); mortality: 9 â€‹%]. The DELAY group had longer LOS (39 vs 32 days, p â€‹< â€‹0.001). There was no significant difference in unnecessary gastrostomy rate between groups (p â€‹= â€‹0.1331). In adjusted hazard analysis, SYNC predicted shorter LOS (HR:1.54; 95 â€‹% CI:1.20-1.98, p â€‹< â€‹0.001). CONCLUSIONS: Synchronous gastrostomy was associated with shorter length of stay and similar rates of unnecessary gastrostomy in TBI patients.

CASE FATALITY RATE OF CHILDHOOD TUBERCULOSIS: EXPERIENCE FROM FEDERAL TEACHING HOSPITAL GOMBE: A TWO DECADE REVIEW.

Introduction: Tuberculosis (TB) was the leading cause of death from an infectious agent worldwide, until the Coronavirus (COVID-19) pandemic, ranking above HIV/AIDS. Nigeria ranks 6th among the 30 TB high-burden countries (TB, TB/HIV, DRTB) and 1st in Africa. The estimated case fatality rate (CFR) of TB in Sub-Sahara Africa (SSA) is 15%. Objective: To review the Tuberculosis case fatality rate (TCFR) in children diagnosed with TB from 2000-2019 in Federal Teaching Hospital Gombe. Methodology: All cases of Tuberculosis (TB) diagnosed in children using ICD 10 classification were retrieved and analyzed. These included deaths from TB. The mainstay of TB diagnosis was clinical using TB Score (81%), Gene Xpert was 7%, and AFB was 10%. Results: 26,716 children were admitted; 383 had TB out of which 208(54.3%) were males and 175 (45.7%) females. TB constituted 1.4% of Paediatric admissions. Children 0 -5 years constituted 46.7% (179/383) of cases and 11 - 18 years were 31.3% (120/383). Fulani, Hausa, and Tangale constituted 43.6% (167), 21.1% (81), and 6.8% (26) of TB cases respectively. TB admissions were highest between 2015 and 2019 (31.8%). TB adenitis was the most common extrapulmonary TB. Tuberculosis/HIV co-infection accounted for 103(27%), out of which 74% (44) died. Overall TCFR was 15.6%; TCFR was 16.3% in males and 14.8% in females. The TCFR was 46.7% in 0-5yrs; 15% in 6-9yrs and 38.3% in 10-18yrs.Fulani had the highest CFR (11.9%). Tuberculosis CFR was highest between 2010-2014 (30.0%) and lowest in 2005-2009 (21.6%). Conclusion: The Tuberculosis CFR is comparable to SSA CFR.

REVEALING THE VARIED REALITY OF MALARIA-RELATED DEATHS IN CHILDREN ACROSS GENDER, AGE, AND ETHNICITY IN FEDERAL TEACHING HOSPITAL GOMBE OVER 20 YEARS: AN ESSENTIAL EPIDEMIOLOGIC IMPERATIVE.

Introduction: Nigeria recorded 31% of 619,000 malaria deaths globally and accounts for 25-30% of all childhood mortality in the country. Few studies in Nigeria, have reported malaria's case fatality rate over a long period. Objective: To determine Malaria Case Fatality Rate among Children admitted from 2000-2019. Methodology: All severe malaria cases and deaths amongst children aged 0-18 over the last two decades were analysed using ICD-10. The diagnosis was based on clinical and microscopic findings. Results: 26,716 children were admitted, 2494 (9.3%) were diagnosed with malaria and 209 died. Malaria constituted 5.3% (209/3956) of all childhood mortality. Males constituted 58.9 % (1468/2494) while 65% (1642/2494) were aged 0-5 years. Of the malaria admissions, Fulani and Hausa constituted 948(38%) and 438(17.6%) respectively. Admissions were highest in October (15%) and in 2012 (9.6%). The overall malaria CFR was 8.3%; 8.8% in Females (91/1026) and 8.03% in Males P-value <0.05 (X2=54.735); 8.6% in children aged 0-5years, 8.2% in 6-10 years and 7.4% in 11-18 years, P-value <0.05 (X2=893.164). CFR was highest in April (11.4%)and lowest in November (5.2%). Kanuri and Igbo had CFR of 70% and 38.4% respectively while it was lowest in Tera tribe (4.3%), P-value<0.05. The CFR was highest in the year 2004 (22%), 3.5% in 2000 and 2006. Over the years, case fatality rate was 15.9% between 2000-2004, 6.1% from 2005-2009. Between 2010-2015, it was 7.3% and 8.5% from 2016-2019. Conclusion: This study revealed the deadly reality of severe malaria with increased CFR among females, aged 0-5 and the Kanuri tribe.

DIAGNOSIS DISCLOSURE RATE AND ITS ASSOCIATIONS AMONG ADOLESCENTS LIVING WITH HUMAN IMMUNODEFICIENCY VIRUS IN GOMBE METROPOLIS, NIGERIA.

Introduction: Disclosure of Human Immunodeficiency Virus (HIV) status is one of the major challenges in the management of children and adolescents living with HIV (CALHIV). With the increasing number of adolescents living with HIV (ALHIV) and the peculiarities of the adolescent stage of development, there is a need for local data on the disclosure of HIV status among adolescents living with HIV in our area of practice. Objectives: To determine the prevalence of disclosure of HIV status and its associated factors among Adolescents living with HIV in Gombe Metropolis. Methodology: This was a cross-sectional descriptive study among 130 ALHIV aged 12-18 years, attending Antiretroviral Therapy (ART) clinics in Federal Teaching Hospital and State Specialist Hospital- Gombe who were recruited consecutively over 10 months. Disclosure of HIV status was assessed using a pre-tested semi-structured questionnaire in both the adolescents and their respective caregivers. Results: The prevalence of HIV status disclosure by caregivers' report and self-report was 66.2% and 63.1% respectively. Older adolescents' age and a higher level of education were significantly associated with disclosure (p value < 0.05). The commonest reason for disclosure was 'increasing curiosity' 23/130(26.7%) while 'being too young' was the commonest reason for non-disclosure 19/44(43.2%). About half 42/86(48.8%) of the disclosures were done by the mothers while 15/86(17.4%) disclosure processes were carried out by healthcare workers. Conclusion: The disclosure rate was relatively high among ALHIV in the Gombe Metropolis. Caregivers should be encouraged on early disclosure.

EPIDEMIOLOGIC TREND AND CASE FATALITY OF CHILDHOOD TETANUS IN FEDERAL TEACHING HOSPITAL GOMBE; A 20YEARS REVIEW.

Introduction: Tetanus is a vaccine-preventable disease, it remains a significant cause of morbidity and mortality in both neonatal and post-neonatal periods, especially in developing countries with limited health facilities and inadequate vaccination. The overall case fatality rate (CFR) is 13.2% globally, highest in the neonatal period and in sub-Saharan Africa. CFR is 64%, 47%, and 43% in Nigeria, Uganda, and Tanzania respectively. Objectives: To determine the Case Fatality Rate of Childhood tetanus in FTHG from 2000-2019. Methodology: All cases and deaths from tetanus amongst children aged 0-18 years in paediatric medical ward of FTHG over the last two decades diagnosed clinically and classified using ICD-10 were analysed. Results: 95 cases of tetanus out of 26,716 total admissions constituting 0.004%. There were 49 tetanus deaths out of 3956 total childhood deaths (0.012%) over the study period. Males constituted 66% (63/95). 30% (28/95) were aged 0-28 days; 23.1% (22/95) were adolescents. Fulani and Hausa constituted 37% (34/95) and 31% (29/95) respectively. Admission was highest in the dry season 52% (50/95 %). The overall tetanus CFR was 51.6%; 78% of deaths were in males (38/49), 30% in neonates, and 23% in adolescents. CFR was highest during the dry season (67.3%). Hausa and Fulani had CFR of 51% and 40% respectively. P-value <0.05 The CFR was 88% between 2000-2004, 72% from 2005-2009, 71% between 2010-2014 and 33% from 2015-2019. Conclusion: Tetanus CFR is still high among neonates and adolescents. Maternal tetanus vaccine and booster doses in children need strengthening.

IN-PATIENT PNEUMONIA BURDEN AND CASE FATALITY RATES IN CHILDREN OVER TWO DECADES IN FEDERAL TEACHING HOSPITAL, GOMBE (FTHG).

Introduction: Pneumonia is the leading cause of death among children globally accounting for an estimated 1.2 million (18%) total deaths annually. The number of childhood-related deaths from pneumonia is approximately 2000-fold higher in developing than in developed countries. Nigeria contributes the highest of pneumonia-related deaths globally. Objectives: To determine the case fatality rates (CFR) of pneumonia from 2000-2019 in paediatric ward, FTHG. Methodology: All cases of pneumonia admissions and deaths in patients aged 0-18 years, using ICD-10 classification, were retrieved and analysed. The mainstay of diagnosis is clinical and/or radiographic features. Results: A total of 26,716 children were admitted during this period, 1151 had pneumonia (4.3%) and 118 died. Males constituted 647 (56.2%) and females 43.8% of the total pneumonia admissions. Children aged 0-5 years had the highest pneumonia admissions, followed by 6-9 years. Admissions were highest in the wet than the dry season. Pneumonia CFR was 10.2%; 10.9% in females and 9.7% in males. Under-5 constituted 84% (969/1151) of pneumonia admission with a CFR of 9.3%. CFR were 10.3% and 21% in 6-10 years, and 11-18 years respectively. The CFR between2000-2004 was 14.1%, 2005-2009:21.1%, 2010-2014:10.2% and 2015-2019:7.2%. Kanuri had the highest CFR of 56.2%.(P <0.05) Other ethnic groups were 29.4% in Waja, 25% in Tula, 21.4% in Igbo, 16.6% in Yoruba, 12.1% in Tangale, 10.2% in Hausa, 8.8%in Bolewa and 8.3% in Fulani. The CFR was highest in February20.2%. Conclusion: Pneumonia Case fatality is high.

Acetyl-methyllysine marks chromatin at active transcription start sites.

Lysine residues in histones and other proteins can be modified by post-translational modifications that encode regulatory information1. Lysine acetylation and methylation are especially important for regulating chromatin and gene expression2-4. Pathways involving these post-translational modifications are targets for clinically approved therapeutics to treat human diseases. Lysine methylation and acetylation are generally assumed to be mutually exclusive at the same residue. Here we report cellular lysine residues that are both methylated and acetylated on the same side chain to form Nε-acetyl-Nε-methyllysine (Kacme). We show that Kacme is found on histone H4 (H4Kacme) across a range of species and across mammalian tissues. Kacme is associated with marks of active chromatin, increased transcriptional initiation and is regulated in response to biological signals. H4Kacme can be installed by enzymatic acetylation of monomethyllysine peptides and is resistant to deacetylation by some HDACs in vitro. Kacme can be bound by chromatin proteins that recognize modified lysine residues, as we demonstrate with the crystal structure of acetyllysine-binding protein BRD2 bound to a histone H4Kacme peptide. These results establish Kacme as a cellular post-translational modification with the potential to encode information distinct from methylation and acetylation alone and demonstrate that Kacme has all the hallmarks of a post-translational modification with fundamental importance to chromatin biology.

Elevational surveys of Sulawesi herpetofauna 1: Gunung Galang, Gunung Dako Nature Reserve.

The Indonesian island of Sulawesi has a unique geology and geography, which have produced an astoundingly diverse and endemic flora and fauna and a fascinating biogeographic history. Much biodiversity research has focused on the regional endemism in the island's Central Core and on its four peninsulas, but the biodiversity of the island's many upland regions is still poorly understood for most taxa, including amphibians and reptiles. Here, we report the first of several planned full-mountain checklists from a series of herpetological surveys of Sulawesi's mountains conducted by our team. In more than 3 weeks of work on Gunung Galang, a 2,254 m peak west of the city of Tolitoli, Sulawesi Tengah Province, on Sulawesi's Northern Peninsula, we recovered nearly fifty species of reptiles and amphibians, more than a dozen of which are either new to science or known but undescribed. The incompleteness of our sampling suggests that many more species remain to be discovered on and around this mountain.

Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry.

RNA metabolic labeling using 4-thiouridine (s4U) captures the dynamics of RNA synthesis and decay. The power of this approach is dependent on appropriate quantification of labeled and unlabeled sequencing reads, which can be compromised by the apparent loss of s4U-labeled reads in a process we refer to as dropout. Here we show that s4U-containing transcripts can be selectively lost when RNA samples are handled under sub-optimal conditions, but that this loss can be minimized using an optimized protocol. We demonstrate a second cause of dropout in nucleotide recoding and RNA sequencing (NR-seq) experiments that is computational and downstream of library preparation. NR-seq experiments involve chemically converting s4U from a uridine analog to a cytidine analog and using the apparent T-to-C mutations to identify the populations of newly synthesized RNA. We show that high levels of T-to-C mutations can prevent read alignment with some computational pipelines, but that this bias can be overcome using improved alignment pipelines. Importantly, kinetic parameter estimates are affected by dropout independent of the NR chemistry employed, and all chemistries are practically indistinguishable in bulk, short-read RNA-seq experiments. Dropout is an avoidable problem that can be identified by including unlabeled controls, and mitigated through improved sample handing and read alignment that together improve the robustness and reproducibility of NR-seq experiments.