bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of adherence to preoperative fasting guidelines and associated patient discomfort in adult elective surgical patients in public hospitals of Addis Ababa, Ethiopia: a multicenter cross-sectional study
Authors: Fekede Mulualem S. , Abebe Bereket A. , Awol Meron A.
Published: February 2023

Background:

Preoperative fasting is compulsory before anesthesia to lower the risk of pulmonary aspiration. However, it is usually prolonged beyond the recommended time affecting the patient’s comfort and has several deleterious effects.

Objective:

To assess the adherence to preoperative fasting guidelines and associated patient discomfort in adult elective surgical patients in public hospitals of Addis Ababa, Ethiopia.

Materials and methods:

A multicenter cross-sectional study was conducted on 422 adult patients who underwent elective surgery at Addis Ababa public hospitals from February 20, to May 10, 2021. The collected data were entered into SPSS, version 24 for analysis. Spearman correlation and independent t test were used to assess the relationship between preoperative fasting time and explanatory variables, as appropriate. P value <0.05 was considered as statistically significant.

Results:

Majority (97.4%) of patients were instructed to fast from midnight regardless of the food type and schedule. Majority (98.1%) of the participants did not adhere to the preoperative fasting guidelines. The mean preoperative fasting time was 14.26±2.35 hours (range: 8–22 h) for solid foods and 13.89±2.37 hours (range: 8–21 h) for clear fluids. More than half (64%) of the participants felt preoperative discomfort, and factors contributing were thirst, hunger, mouth dryness, lengthy waiting of prior surgery, and tiredness. There was a moderate positive correlation between preoperative fasting time and severity of patient discomfort (P<0.001). There was also a strong positive correlation between total fasting time and the sequence of patient’s schedule (P<0.001).

Conclusions:

Preoperative fasting for solids and clear liquids was longer than the recommended international fasting guidelines. Preoperative fasting duration had an association with preoperative discomforting factors. Incorrect orders of instructions and changing sequences of schedule challenged the preoperative fasting adherence. Thus, preoperative fasting instructions should be clear, individualized; and health professionals need to communicate when surgery is delayed or changed.
Patient and Graft Survival After A1/A2-incompatible Living Donor Kidney Transplantation
Authors: Bisen Shivani S. , Getsin Samantha N. , Chiang Po-Yu , Herrick-Reynolds Kayleigh , Zeiser Laura B. , Yu Sile , Desai Niraj M. , Al Ammary Fawaz , Jackson Kyle R. , Segev Dorry L. , Massie Allan B.
Published: February 2023

Background.

ABO type B and O kidney transplant candidates have increased difficulty identifying a compatible donor for living donor kidney transplantation (LDKT) and are harder to match in kidney paired donation registries. A2-incompatible (A2i) LDKT increases access to LDKT for these patients. To better inform living donor selection, we evaluated the association between A2i LDKT and patient and graft survival.

Methods.

We used weighted Cox regression to compare mortality, death-censored graft failure, and all-cause graft loss in A2i versus ABO-compatible (ABOc) recipients.

Results.

Using Scientific Registry of Transplant Recipients data 2000–2019, we identified 345 A2i LDKT recipients. Mortality was comparable among A2i and ABOc recipients; weighted 1-/5-/10-y mortality was 0.9%/6.5%/24.2%, respectively, among A2i LDKT recipients versus 1.4%/7.7%/22.2%, respectively, among ABOc LDKT recipients (weighted hazard ratio [wHR], 0.811.041.33; P = 0.8). However, A2i recipients faced higher risk of death-censored graft failure; weighted 1-/5-/10-y graft failure was 5.7%/11.6%/22.4% for A2i versus 1.7%/7.5%/17.2% for ABOc recipients (wHR in year 1 = 2.243.565.66; through year 5 = 1.251.782.53; through year 10 = 1.151.552.07). By comparison, 1-/5-/10-y wHRs for A1-incompatible recipients were 0.631.966.08/0.390.942.27/0.390.831.74.

Conclusions.

A2i LDKT is generally safe, but A2i donor/recipient pairs should be counseled about the increased risk of graft failure and be monitored as closely as their A1-incompatible counterparts posttransplant.
Development of a mobile laboratory system in hydrogen fuel cell buses and evaluation of the performance for COVID-19
Authors: Okude Miho , Suzuki Kenji , Naito Asami , Ebashi Akio , Kusama Tomoka , Kiyotaki Junichi , Akashi Yusaku , Kiyasu Yoshihiko , Kurihara Yoko , Notake Shigeyuki , Takanashi Masaki , Setoyama Tomokazu , Kawakami Yasushi , Suzuki Hiromichi
Published: February 2023

Introduction

We newly designed and developed two types of hydrogen fuel cell (HFC) buses (motorcoach type and minibus type) with a mobile laboratory system. Feasibility studies have been performed for mobile laboratory testing, especially for the laboratory performance of COVID-19 RT-PCR (PCR).

Methods

We evaluated the driving range capability, PCR sample size capacity, turn-around time (TAT), and analytical performance for the detection of SARS-CoV-2. Saliva samples were used for the current research and the analytical performance was compared with reference PCR.

Results

The estimated driving range and sample size capacity were 432 km and 3,258 samples, respectively for the HFC motorcoach and 313 km and 2,146 samples for the HFC minibus, respectively. For the TAT, the median time between the sample submission and the completion of PCR were 86 min for the motorcoach and 76 min for the minibus, and the median time between sample submission and the electronic reporting of the result to each visitor were 182 min for the motorcoach and 194 min for the minibus. A secondary analysis of 1,574 HFC mobile laboratory testing samples was conducted and all negative samples were negative by reference PCR. Furthermore, all positive samples were confirmed as positive by reference PCR or other molecular examinations.

Conclusion

We confirmed the feasibility of HFC mobile laboratory systems for achieving the rapid reporting of highly accurate PCR results.
Data-driven neuropathological staging and subtyping of TDP-43 proteinopathies
Authors: Young Alexandra L , Vogel Jacob W , Robinson John L , McMillan Corey T , Ossenkoppele Rik , Wolk David A. , Irwin David J. , Elman Lauren , Grossman Murray , Lee Virginia M-Y , Lee Edward B , Hansson Oskar
Published: February 2023

TAR DNA-binding protein-43 (TDP-43) accumulation is the primary pathology underlying several neurodegenerative diseases. Charting the progression and heterogeneity of TDP-43 accumulation is necessary to better characterise TDP-43 proteinopathies, but current TDP-43 staging systems are heuristic and assume each syndrome is homogeneous. Here, we use data-driven disease progression modelling to derive a fine-grained empirical staging system for the classification and differentiation of frontotemporal lobar degeneration due to TDP-43 (FTLD-TDP, n=126), amyotrophic lateral sclerosis (ALS, n=141) and limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) with and without Alzheimer’s disease (n=304). The data-driven staging of ALS and FTLD-TDP complement and extend previously described human-defined staging schema for ALS and behavioural variant frontotemporal dementia. In LATE-NC individuals, progression along data-driven stages was positively associated with age, but negatively associated with age in individuals with FTLD-TDP. Using only regional TDP-43 severity, our data driven model distinguished individuals diagnosed with ALS, FTLD-TDP or LATE-NC with a cross-validated accuracy of 85.9%, with misclassifications associated with mixed pathological diagnosis, age and genetic mutations. Adding age and SuStaIn stage to this model increased accuracy to 92.3%. Our model differentiates LATE-NC from FTLD-TDP, though some overlap was observed between late-stage LATE-NC and early-stage FTLD-TDP. We further tested for the presence of subtypes with distinct regional TDP-43 progression patterns within each diagnostic group, identifying two distinct cortical-predominant and brainstem-predominant subtypes within FTLD-TDP and a further two subcortical-predominant and corticolimbic-predominant subtypes within ALS. The FTLD-TDP subtypes exhibited differing proportions of TDP-43 type, while there was a trend for age differing between ALS subtypes. Interestingly, a negative relationship between age and SuStaIn stage was seen in the brainstem/subcortical-predominant subtype of each proteinopathy. No subtypes were observed for the LATE-NC group, despite aggregating AD+ and AD-individuals and a larger sample size for this group. Overall, we provide an empirical pathological TDP-43 staging system for ALS, FTLD-TDP and LATE-NC, which yielded accurate classification. We further demonstrate that there is substantial heterogeneity amongst ALS and FTLD-TDP progression patterns that warrants further investigation in larger cross-cohort studies.
Mosquito repellent efficacy of Australian Blue CypressCallitris intratropicaessential oil and its topical formulation under laboratory and field conditions
Authors: Koinari Melanie , Amos Brogan , Townsend Michael , Karl Stephan
Published: February 2023

Mosquito repellents are important for personal protection against nuisance and potentially infectious mosquito bites. Repellent activity of Australian Blue Cypress (ABC) essential oil and a commercially formulated skin lotion containing ABC oil were compared with 20% DEET (N, N-diethyl-3methylbenzamide) and evaluated against mosquitoes under laboratory and field conditions in North Queensland, Australia. Using the arm-in-cage method, the following cumulative doses of ABC oil in ethanol were tested; 0.5%, 1.5%, 3%, 5%, 7.5% and 10.5% against femaleAedes aegypti. In the field, 2.5%, 5% and 10% of diluted ethanolic ABC oil were tested using the human landing catch method. We observed a dose-dependent increase in protection with diluted ABC oil approaching 80% at high concentrations. While some protection was afforded, mosquito landing and probing was still recorded immediately after application (laboratory) for both ABC essential oil and skin lotion. Protection declined from 80 – 70% and 93 – 50% for 20% ABC oil (laboratory) and 10% ABC oil (highest dose, field), respectively. For the formulated product, protection declined from 85 – 75% in the laboratory and from 63 – 50% in the field. To conclude, both ABC essential oil and the formulated skin lotion provided moderate protection against mosquito bites, which decreased soon after application.
Simvastatin therapy in different subtypes of hypercholesterolemia – a physiologically based modelling approach
Authors: Bartsch Florian , Grzegorzewski Jan , Pujol Helena Leal , Tautenhahn Hans-Michael , König Matthias
Published: February 2023

Hypercholesterolemia is a multifaceted plasma lipid disorder with heterogeneous causes including lifestyle and genetic factors. A key feature of hypercholesterolemia is elevated plasma levels of low-density lipoprotein cholesterol (LDL-C). Several genetic variants have been reported to be associated with hypercholesterolemia, known as familial hypercholesterolemia (FH). Important variants affect the LDL receptor (LDLR), which mediates the uptake of LDL-C from the plasma, apoliporotein B (APOB), which is involved in the binding of LDL-C to the LDLR, and proprotein convertase subtilisin/kexin type 9 (PCSK9), which modulates the degradation of the LDLR. A typical treatment for hypercholesterolemia is statin medication, with simvastatin being one of the most commonly prescribed statins. In this work, the LDL-C lowering therapy with simvastatin in hypercholesterolemia was investigated using a computational modeling approach. A physiologically based pharmacokinetic model of simvastatin integrated with a pharmacodynamic model of plasma LDL-C (PBPK/PD) was developed based on extensive data curation. A key component of the model is LDL-C turnover by the liver, consisting of: hepatic cholesterol synthesis with the key enzymes HMG-CoA reductase and HMG-CoA synthase; cholesterol export from the liver as VLDL-C; de novo synthesis of LDLR; transport of LDLR to the membrane; binding of LDL-C by LDLR via APOB; endocytosis of the LDLR-LDL-C complex; recycling of LDLR from the complex. The model was applied to study the effects of simvastatin therapy in hypercholesterolemia due to different causes in the LDLR pathway corresponding to different subtypes of hypercholesterolemia. Model predictions of LDL-C lowering therapy were validated with independent clinical data sets. Key findings are: (i) hepatic LDLR turnover is highly heterogeneous among FH classes; (ii) despite this heterogeneity, simvastatin therapy results in a consistent reduction in plasma LDL-C regardless of class; and (iii) simvastatin therapy shows a dose-dependent reduction in LDL-C. Our model suggests that the underlying cause of hypercholesterolemia does not influence simvastatin therapy. Furthermore, our model supports the treatment strategy of stepwise dose adjustment to achieve target LDL-C levels. Both the model and the database are freely available for reuse.
Structural basis for guide RNA selection by the RESC1-RESC2 complex
Authors: Dolce Luciano G. , Nesterenko Yevheniia , Walther Leon , Weis Félix , Kowalinski Eva
Published: February 2023

Kinetoplastid parasites, such as trypanosomes or leishmania, rely on RNA-templated RNA editing to mature mitochondrial cryptic pre-mRNAs into functional protein-coding transcripts. Processive pan-editing of multiple editing blocks within a single transcript is dependent on the 20-subunit RNA editing substrate binding complex (RESC) that serves as a platform to orchestrate the interactions between pre-mRNA, guide RNAs (gRNAs), the catalytic RNA editing complex (RECC), and a set of RNA helicases. Due to the lack of molecular structures and biochemical studies with purified components, neither the spacio-temporal interplay of these factors nor the selection mechanism for the different RNA components is understood. Here we report the cryo-EM structure ofTrypanosoma bruceiRESC1-RESC2, a central hub module of the RESC complex. The structure reveals that RESC1 and RESC2 form an obligatory domain-swapped dimer. Although the tertiary structures of both subunits closely resemble each other, only RESC2 selectively binds 5’-triphosphate-nucleosides, a defining characteristic of gRNAs. We therefore propose RESC2 as the protective 5’-end binding site for gRNAs within the RESC complex. Overall, our structure provides a starting point for the study of the assembly and function of larger RNA-bound kinetoplast RNA editing modules and might aid in the design of anti-parasite drugs.

Key findings

The kinetoplastid mitochondrial RNA editing factors RESC1 and RESC2 resemble a group of capping enzymes that are only found in protozoans, fungi and viruses.

RESC1 and RESC2 lack the typical catalytic residues, and only RESC2 can bind a triphosphate-nucleoside.

We propose that the RESC1-RESC2 dimer selects guide RNAs based on their 5’-triphosphate and serves as a protective 5’-end binding complex.
Staphylococcus aureusfunctional amyloids catalyze degradation of β-lactam antibiotics
Authors: Arad Elad , Golan Nimrod , Rapaport Hanna , Landau Meytal , Jelinek Raz
Published: February 2023

Antibiotic resistance of bacteria is considered one of the most alarming developments in modern medicine. While varied pathways for bacteria acquiring antibiotic resistance have been identified, there still are open questions concerning the mechanisms underlying resistance. Here, we show that alpha phenol-soluble modulins (PSMα’s), functional bacterial amyloids secreted byStaphylococcus aureus, catalyze breakup of β-lactams, a prominent class of antibiotic compounds. Specifically, we show that PSMα2 and, particularly, PSMα3 catalyze hydrolysis of the amide-bond four-member ring of nitrocefin, a widely used β-lactam surrogate. Microscopic and spectroscopic analyses of several PSMα3 variants and correlation with their catalytic activities allowed mapping of the catalytic sites on the amyloid fibrils’ surface, specifically underscoring the key roles of the cross-α fibril organization, and the combined electrostatic and nucleophilic functions of the lysine residue array. This study unveils a previously unknown role of functional bacterial amyloids as catalytic agents for antibiotic compounds, pointing to possible mechanisms for antibiotic resistance of bacteria.

ToC Graphical Abstract
Spermidine Is The Main Polyamine Required By Intracellular Parasites For Survival Within Host Erythrocytes
Authors: Singh Pallavi , Mamoun Choukri Ben
Published: February 2023

Intracellular eukaryotic pathogens such asBabesiaandPlasmodium, the agents of human babesiosis and malaria, require salvage or de novo synthesis of several nutrients for survival in human erythrocytes. One such nutrient is putrescine, which is either transported from the host or synthesized from ornithine and serves as a precursor for the biosynthesis of two other polyamines: spermidine and spermine. However, the specific polyamines required by these parasites for survival and the molecular process they control remain unknown. We show in bothB. duncaniandP. falciparumthat spermidine is the main product of the polyamine biosynthesis machinery required for parasite survival. Simultaneous inhibition of spermidine synthesis from putrescine and catabolism from spermine results in cell death and parasite survival can only be rescued by spermidine. Finally, we demonstrate that spermidine’s essential function in these parasites is through regulation of protein translation via hypusination of the translation initiation factor eIF5A.
Quantification of gallium cryo-FIB milling damage in biological lamella
Authors: Lucas Bronwyn A. , Grigorieff Nikolaus
Published: February 2023

Cryogenic electron microscopy (cryo-EM) has the potential to reveal the molecular details of biological processes in their native, cellular environment at atomic resolution. However, few cells are sufficiently thin to permit imaging with cryo-EM. Thinning of frozen cells to <500 nm lamellae by cryogenic focused ion beam (FIB) milling has enabled visualization of cellular structures with cryo-EM. FIB-milling represents a significant advance over prior approaches because of its ease of use, scalability, and lack of large-scale sample distortions. However, the amount of damage caused by FIB-milling to the generated thin cell section has not yet been determined. We recently described a new approach for detecting and identifying single molecules in cryo-EM images of cells using 2D template matching (2DTM). 2DTM is sensitive to small differences between a molecular model (template) and the detected structure (target). Here we use 2DTM to demonstrate that under the standard conditions used for machining lamellae of biological samples, FIB-milling introduces a layer of variable damage that extends to a depth of 60 nm from each lamella surface. This thickness exceeds previous estimates and limits the recovery of information forin situstructural biology. We find that the mechanism of FIB-milling damage is distinct from radiation damage during cryo-EM imaging. By accounting for both electron scattering and FIB-milling damage, we find that FIB-milling damage will negate the potential improvements from lamella thinning beyond 90 nm.

Significance

The molecular mechanisms of biological macromolecules and their assemblies is often studied using purified material. However, the composition, conformation and function of most macromolecules depend on their cellular context, and therefore, must also be studied inside cells. Focused ion beam (FIB) milling enables cryogenic electron microscopy to visualize macromolecules in cells at close to atomic resolution by generating thin sections of frozen cells. However, the extent of FIB-milling damage to frozen cells is unknown. Here we show that Ga+FIB-milling introduces damage to a depth of ∼60 nm from each lamella surface, leading to a loss of recoverable information of up to 20% in 100 nm samples. FIB-milling with Ga+therefore presents both an opportunity and an obstacle for structural cell biology.
Frequency variation and dose modification of benznidazole administration for the treatment ofTrypanosoma cruziinfection in mice, dogs and non-human primates
Authors: Bustamante Juan M. , White Brooke E. , Wilkerson Gregory K. , Hodo Carolyn L. , Auckland Lisa D. , Wang Wei , McCain Stephanie , Hamer Sarah A. , Saunders Ashley B. , Tarleton Rick L.
Published: February 2023

Trypanosoma cruzinaturally infects a broad range of mammalian species and frequently results in the pathology that has been most extensively characterized in human Chagas disease. Currently employed treatment regimens fail to achieve parasitological cure ofT. cruziinfection in the majority of cases. In this study, we have extended our previous investigations of more effective, higher dose, intermittent administration protocols using the FDA-approved drug benznidazole (BNZ), in experimentally infected mice and in naturally infected dogs and non-human primates (NHP). Collectively these studies demonstrate that twice-weekly administration of BNZ for more than 4 months at doses that are ∼2.5-fold that of previously used daily dosing protocols, provided the best chance to obtain parasitological cure. Dosing less frequently or for shorter time periods was less dependable in all species. Prior treatment using an ineffective dosing regimen in NHPs did not prevent the attainment of parasitological cure with an intensified BNZ dosing protocol. Furthermore, parasites isolated after a failed BNZ treatment showed nearly identical susceptibility to BNZ as those obtained prior to treatment, confirming the low risk of induction of drug resistance with BNZ and the ability to adjust the treatment protocol when an initial regimen fails. These results provide guidance for the use of BNZ as an effective treatment forT. cruziinfection and encourage its wider use, minimally in high value dogs and at-risk NHP, but also potentially in humans, until better options are available.
Regulation of Bacterial Two-Component Systems by Cardiolipin
Authors: Yeo Won-Sik , Dyzenhaus Sophie , Torres Victor J , Brinsmade Shaun R , Bae Taeok
Published: February 2023

The composition of phospholipid membranes is critical to regulating the activity of membrane proteins for cellular functions. Cardiolipin is a unique phospholipid present within the bacterial membrane and mitochondria of eukaryotes and plays a role in maintaining the function and stabilization of membrane proteins. Here, we report that, in the human pathogen Staphylococcus aureus, cardiolipin is required for full activity of the SaeRS two-component system (TCS). Deletion of the cardiolipin synthase genes,cls1, andcls2, reduces the basal activity of SaeRS and other TCSs. Cardiolipin is an indispensable requisite for Sae activation mediated by human neutrophil peptides (HNPs) in the stationary growth phase but not mandatory for Sae induction in the exponential growth phase. Ectopic expression withcls2, but not withcls1, in thecls1 cls2double mutant fully restores Sae activity. Elimination of cardiolipin from the membranes results in decreased kinase activity of the sensor protein SaeS. Purified SaeS protein directly binds to cardiolipin as well as phosphatidylglycerol. A strain lackingcls2orcls1cls2rendersS. aureusless cytotoxic to human neutrophils and less virulent in a mouse model of infection. Our findings suggest that cardiolipin enables a pathogen to confer virulence by modulating the kinase activity of SaeS and other sensor kinases upon infection.
Sexually transmitted infection knowledge levels, socio-demographic characteristics and sexual behaviour among men who have sex with men: results from a cross-sectional survey in Nairobi, Kenya
Authors: Nyasani Delvin Kwamboka , Onyambu Meshack , Lunani Laura Lusike , Oino Geoffrey Ombati , Mutua Gaundensia Nzembi , Price Matt , Osero Justus.O.
Published: February 2023

Background

High rates of sexually transmitted infections (STIs) among men who have sex with men (MSM) have been reported, there is little research on their STI knowledge. Our study sought to characterize knowledge and awareness of STIs among MSM in Nairobi, Kenya.

Methods

We mobilized MSM aged ≥18 years from Nairobi into a cross-sectional study. To determine their understanding about STIs, a pre-tested structured questionnaire was administered. Knowledge score was generated by summing up the number of responses answered correctly by a participant. We dichotomized scores as “low” and “high”, by splitting the group at <12 and ≥12 which was the mean.

Results

A total of 404 participants were interviewed between the month of March and August 2020. The mean age was 25.2 (SD=6.4) years. Majority were single (80.4%) and Christians (84.2%). All participants had some formal education ranging from primary to tertiary; the majority (92.3%) had secondary education or more. Most (64.0%) were employed and their monthly income ranged from <50->150 USD. Almost all (98.5%) were Kenyans.

Of the 404 (90.6%) self-identified as male and (47.5%) reported to be exclusively top partners. Many (39.9%) reported being both bottom and top, while those reporting to be bottom partners were, (12.6%). The last 12 months, (55.4%) of the participants reported having sex with men only and (88.6%) reported to have had more than one sexual partner.

Participants scored an average of 12.2, out of 29 SD 4.5. The multivariable modelling revealed that participants aged ≥25 years were more likely to have a higher knowledge score compared with the participants aged 18-24 years (aOR=0.973, CI: 0.616-1.538). Regarding education and occupation, participants who had tertiary education and those who were employed were more likely to have a higher knowledge score compared with the participants who had primary education and were not employed (aOR=2.627, CI:1.142-6.043) (aOR=0.922, CI:0.401-2.117). Participants who were earning (USD >150) were more likely to have a higher knowledge score compared to the ones who were not earning (aOR=2.520, CI: 0.900-7.055). Further bisexual men were more likely to have a higher knowledge score compared with the participants who were having sex with men only (aOR= 1.550, CI: 1026-2.342)

Conclusion

Participant’s knowledge level regarding STIs was low. We recommend health care workers to continue educating patients about STIs.
Subcellular second messenger networks drive distinct repellent-induced axon behaviors
Authors: Baudet S , Zagar Y , Roche F , Gomez Bravo C , Couvet S , Bécret J , Belle M , Ros O , Nicol X
Published: February 2023

Abstract

Second messengers, including cAMP, cGMP and Ca2+are often placed in an integrating position to combine the extracellular cues that orient growing axons in the developing brain. This view suggests that axon repellents share the same set of cellular messenger signals and that axon attractants evoke opposite cAMP, cGMP and Ca2+changes. Investigating the confinement of these second messengers in cellular nanodomains, we instead demonstrate that two repellent cues, ephrin-A5 and Slit1, induce spatially segregated signals. These guidance molecules activate subcellular-specific second messenger crosstalks, each signaling network controlling distinct axonal morphology changesin vitroand pathfinding decisionsin vivo.
Aberrant light sensing and motility in the green algaChlamydomonas priscuiifrom the ice-covered Antarctic Lake Bonney
Authors: Poirier Mackenzie , Osmers Pomona , Wilkins Kieran , Morgan-Kiss Rachael M. , Cvetkovska Marina
Published: February 2023

The Antarctic green algaChlamydomonas priscuiiis an obligate psychrophile and an emerging model for photosynthetic adaptation to extreme conditions. Endemic to the ice-covered Lake Bonney, this alga thrives at highly unusual light conditions characterized by very low light irradiance (<15 μmol m-2s-1), a narrow wavelength spectrum enriched in blue light, and an extreme photoperiod. Genome sequencing ofC. priscuiiexposed an unusually large genome, with hundreds of highly similar gene duplicates and expanded gene families, some of which could be aiding its survival in extreme conditions. In contrast to the described expansion in the genetic repertoire inC. priscuii, here we suggest that the gene family encoding for photoreceptors is reduced when compared to related green algae. This alga also possesses a very small eyespot and exhibits an aberrant phototactic response, compared to the modelChlamydomonas reinhardtii. We also investigated the genome and behaviour of the closely related psychrophilic algaChlamydomonassp. ICE-MDV, that is found throughout the photic zone of Lake Bonney and is naturally exposed to higher light levels. Our analyses revealed a photoreceptor gene family and a robust phototactic response similar to those in the modelChlamydomonas reinhardtii. These results suggest that the aberrant phototactic response inC. priscuiiis a result of life under extreme shading rather than a common feature of all psychrophilic algae. We discuss the implications of these results on the evolution and survival of shade adapted polar algae.
OH 89: A newly described ∼1.8-million-year-old hominid clavicle from Olduvai Gorge
Authors: Taylor Catherine E , Masao Fidelis , Njau Jackson K , Songita Agustino Venance , Hlusko Leslea J
Published: February 2023

Objectives

Here, we describe the morphology and geologic context of OH 89, a ∼1.8million-year-old partial hominid clavicle from Olduvai (Oldupai) Gorge, Tanzania. We compare the morphology and clavicular curvature of OH 89 to modern humans, extant apes, and a sample of other hominid fossil clavicles.

Materials and Methods

Comparative samples include 25 modern human clavicles, 30Gorilla, 31Pan, 7Papio, and five hominid clavicles. Length regression on midshaft size using the extant comparative samples is used to estimate the total length of OH 89. A set of 9 linear measurements are taken from each individual. We also describe a new methodology for measuring clavicular curvature using measurements of sternal and acromial curvature, from which an overall curvature measurement is calculated. A principal component analysis (PCA) and a t-distributed stochastic neighbor embedding (tSNE) analysis are used to compare the morphology of OH 89 with the extant and fossil comparative samples.

Results

Our new method of measuring clavicular curvature successfully separates the different genera of the extant clavicles. The length estimate and sternal and acromial curve measurements for OH 89 falls within the larger male humans. The PCA shows OH 89 and most of the fossil hominids falling between the modern human andPangroups, while the t-SNE suggests that OH 89, KSD-VP-1/1, KNM-ER 1808, and OH 48 are more similar to each other than to any of the other groups. This analysis also plots KNM-WT 15000 with the modern humans and Krapina 158 with thePanindividuals.

Discussion

The OH 89 clavicle derives from an individual of unknown hominid species with a shoulder breadth similar to that of a large human male. The curvature of OH 89 is relatively human-like relative to its length. Our new methodology for measuring clavicular curvature, combined with the utilization of t-SNE analyses and comparison of t-SNE results to PCA results, provides greater separation of genera than previously used methods, and wider use of t-SNE may be useful in paleoanthropological work.
Modelling the Erythroblastic Island Niche of Dyserythropoietic Anaemia Type IV patients using Induced Pluripotent Stem Cells
Authors: May Alisha , Ventura Telma , Fidanza Antonella , Volmer Helena , Taylor Helen , Romanò Nicola , D’Souza Sunita L , Bieker James J. , Forrester Lesley M.
Published: February 2023

Congenital dyserythropoietic anaemia (CDA) type IV has been associated with an amino acid substitution, Glu325Lys (E325K), in the transcription factor KLF1. These patients present with a range of symptoms, including the persistence of nucleated red blood cells (RBCs) in the peripheral blood which reflects the known role for KLF1 within the erythroid cell lineage. The final stages of RBCs maturation and enucleation take place within the erythroblastic island (EBI) niche in close association with EBI macrophages. It is not known whether the detrimental effects of the E325K mutation in KLF1 are restricted to the erythroid lineage or whether deficiencies in macrophages associated with their niche also contribute to the disease pathology. To address this question, we generated anin vitromodel of the human EBI niche using induced pluripotent stem cells (iPSCs) derived from a CDA type IV patient as well as iPSCs genetically modified to express an KLF1-E325K-ERT2protein that could be activated with 4OH-tamoxifen. CDA patient-derived iPSCs and iPSCs expressing the activated KLF1-E325K-ERT2protein showed significant deficiencies in the production of erythroid cells with associated disruption of some known KLF1 target genes. Macrophages could be generated from all iPSC lines but when the E325K-ERT2fusion protein was activated, we noted the generation of a slightly less mature macrophage population marked by CD93. A subtle reduction in their ability to support RBC maturation was also associated with macrophages carrying the E325K-ERT2transgene. Taken together these data support the notion that the clinically significant effects of the KLF1-E325K mutation are primarily associated with deficiencies in the erythroid lineage but that deficiencies in the niche might have the potential to exacerbate the condition. The strategy we describe provides a powerful approach to assess the effects of other mutations in KLF1 as well as other factors associated with the EBI niche.
Noradrenaline release from the locus coeruleus shapes stress-induced hippocampal gene expression
Authors: Privitera Mattia , von Ziegler Lukas M. , Floriou-Servou Amalia , Duss Sian N. , Zhang Runzhong , Waag Rebecca , Leimbacher Sebastian , Sturman Oliver , Roessler Fabienne K. , Heylen Annelies , Vermeiren Yannick , Van Dam Debby , De Deyn Peter P. , Germain Pierre-Luc , Bohacek Johannes
Published: February 2023

Exposure to an acute stressor triggers a complex cascade of neurochemical events in the brain. However, deciphering their individual impact on stress-induced molecular changes remains a major challenge. Here we combine RNA-sequencing with selective pharmacological, chemogenetic and optogenetic manipulations to isolate the contribution of the locus coeruleus - noradrenaline (LC-NA) system to the acute stress response. We reveal that NA-release during stress exposure regulates a large and reproducible set of genes in the dorsal and ventral hippocampus via β-adrenergic receptors. For a smaller subset of these genes, we show that NA release triggered by LC stimulation is sufficient to mimic the stress-induced transcriptional response. We observe these effects in both sexes, and independent of the pattern and frequency of LC activation. Using a retrograde optogenetic approach, we demonstrate that hippocampus-projecting LC neurons directly regulate hippocampal gene expression. Overall, a highly selective set of astrocyte-enriched genes emerges as key targets of LC-NA activation, most prominently several subunits of protein phosphatase 1 (Ppp1r3c,Ppp1r3d,Ppp1r3g) and type II iodothyronine deiodinase (Dio2). These results highlight the importance of astrocytic energy metabolism and thyroid hormone signaling in LC-mediated hippocampal function and offer new molecular targets for understanding how NA impacts brain function in health and disease.
Glutaredoxin regulation of primary root growth is associated with early drought stress tolerance in pearl millet
Authors: de la Fuente Carla , Grondin Alexandre , Sine Bassirou , Debieu Marilyne , Belin Christophe , Hajjarpoor Amir , Atkinson Jonathan A. , Passot Sixtine , Salson Marine , Orjuela Julie , Tranchant-Dubreuil Christine , Brossier Jean-Rémy , Steffen Maxime , Morgado Charlotte , Dinh Hang Ngan , Pandey Bipin K. , Darmau Julie , Champion Antony , Petitot Anne-Sophie , Barrachina Celia , Pratlong Marine , Mounier Thibault , Nakombo-Gbassault Princia , Gantet Pascal , Gangashetty Prakash , Guédon Yann , Vadez Vincent , Reichheld Jean-Philippe , Bennett Malcolm J. , Kane Ndjido , Guyomarc’h Soazig , Wells Darren M. , Vigouroux Yves , Laplaze Laurent
Published: February 2023

Seedling root traits impact plant establishment under challenging environments. Pearl millet is one of the most heat and drought tolerant cereal crops that provides a vital food source across the sub-Saharan Sahel region. Pearl millet’s early root system features a single fast-growing primary root which we hypothesize is an adaptation to the Sahelian climate. Using crop modelling, we demonstrate that early drought stress is an important constraint in agrosystems in the Sahel where pearl millet was domesticated. Furthermore, we show that increased pearl millet primary root growth is correlated with increased early water stress tolerance in field conditions. Genetics including GWAS and QTL approaches identify genomic regions controlling this key root trait. Combining gene expression data, re-sequencing and re-annotation of one of these genomic regions identified a glutaredoxin-encoding genePgGRXC9as the candidate stress resilience root growth regulator. Functional characterization of its closest Arabidopsis homologAtROXY19revealed a novel role for this glutaredoxin (GRX) gene clade in regulating cell elongation. In summary, our study suggests a conserved function for GRX genes in conferring root cell elongation and enhancing resilience of pearl millet to its Sahelian environment.
Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome
Authors: van Dijk Bram , Farr Andrew D. , Buffard Pauline , Giersdorf Franz , Meijer Jeroen , Dutilh Bas E. , Rainey Paul B.
Published: February 2023

Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome – the zoo of Darwinian replicators that depend on microbial hosts – remains poorly characterised. New experimental approaches and analyses are necessary to advance our understanding beyond simple pairwise MGE-host interactions. To detect horizontal transfer, a bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples, which was then applied to metagenomic data from evolving compost communities. These communities were routinely exposed to an “MGE cocktail” derived from allopatric communities. We show that this results in horizontal transfer of a multitude of previously undetected MGEs, including bacteriophages, phage-plasmids, megaplasmids, and even nanobacteria. Sequences that spread from one community to another are shown to disproportionally carry characteristics of phages and insertion-sequences,i.e., traits of canonically parasitic MGEs. We also show that one particularly prolific mobile element - a 313 kb plasmid – correlates substantially with rates of ammonia production, which under nitrogen limitation is likely beneficial. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the drivers of microbial community evolution.
The vitamin B3analogue nicotinamide riboside has only very minor effects on reducing muscle damage inmdxmice
Authors: Stan Tiberiu Loredan , Vijver Davy v.d. , Verhaart Ingrid E.C. , Aartsma-Rus Annemieke
Published: February 2023

BACKGROUND

Vitamin B3 analogue nicotinamide riboside (NR) has been suggested to have beneficial effects on muscle pathology in a mouse model for Duchenne muscular dystrophy (DMD). In muscle dystrophy, NR is thought to act acts by increasing levels of NAD+, to improve mitochondrial functioning and reduce muscle pathology.

OBJECTIVE

We here aimed to validate the effects of NR to improve muscle quality after eight weeks of treatment in two different mouse models for DMD: the commonly used mdx mouse on a C57BL/10 background (BL10mdx) and the more severely affectedmdxmouse on a DBA/2J background (D2-mdx).

METHODS

To study in more detail whether NR treatment had an impact on muscle pathology, we assessed the expression levels of several markers for DMD pathology (fibrosis, regeneration and inflammation) in diaphragm.

RESULTS

Our data showed a trend for increase in NAD+-levels in blood; only in the D2-mdxNR-treated mice the NAD+-levels were slightly increased. These markers were elevated inmdxmodels compared to controls, but not affected by the NR treatment. Histological analysis of muscle tissues indicated a mild treatment effect in D2-mdxmice.

CONCLUSIONS

Based on our results, testing NR treatment in clinical trials in DMD patients is not warranted.
The influence of parasite load on transcriptional activity and morphology of a cestode and its ant intermediate host
Authors: Sistermans Tom , Hartke Juliane , Stoldt Marah , Libbrecht Romain , Foitzik Susanne
Published: February 2023

Parasites with complex life cycles are known to induce phenotypic changes in their intermediate hosts to increase transmission to the final host. The magnitude of these changes could increase with the number of parasites, which would be beneficial to co-infecting parasites. Yet, adverse effects of high parasite load (i.e., many parasites in a single host) might stress both hosts and parasites (e.g., through an increased immune response). We investigated the consequences of parasite load on the transcriptional activity and morphology of the cestodeAnomotaenia brevisand its intermediate host, the antTemnothorax nylanderi. We demonstrated that many differentially expressed host genes shifted with parasite load, and their functions indicate a stronger immune response and fight against oxidative stress in heavily infected hosts. The expression of other host genes responded to infection in an all-or-nothing manner, as did the morphology of the host workers. However, the cestodes became smaller when they competed with other parasites for resources from a single host. Their expression profile further indicated shifts in host immune avoidance, starvation resistance and vesicle-mediated transport. In summary, our study reveals clear consequences of parasite load and highlights specific processes and traits affected by this.
Graded functional organisation in the left inferior frontal gyrus: evidence from task-free and task-based functional connectivity
Authors: Diveica Veronica , Riedel Michael C. , Salo Taylor , Laird Angela R. , Jackson Rebecca L. , Binney Richard J.
Published: February 2023

The left inferior frontal gyrus (LIFG) has been ascribed key roles in numerous cognitive domains, including language, executive function and social cognition. However, its functional organisation, and how the specific areas implicated in these cognitive domains relate to each other, is unclear. Possibilities include that the LIFG underpins a domain-general function or, alternatively, that it is characterized by functional differentiation, which might occur in either a discrete or a graded pattern. The aim of the present study was to explore the topographical organisation of the LIFG using a bimodal data-driven approach. To this end, we extracted functional connectivity (FC) gradients from 1) the resting-state fMRI time-series of 150 participants (77 female), and 2) patterns of co-activation derived meta-analytically from task data across a diverse set of cognitive domains. We then sought to characterize the FC differences driving these gradients with seed-based resting-state FC and meta-analytic co-activation modelling analyses. Both analytic approaches converged on an FC profile that shifted in a graded fashion along two main organisational axes. An anterior-posterior gradient shifted from being preferentially associated with high-level control networks (anterior LIFG) to being more tightly coupled with perceptually-driven networks (posterior). A second dorsal-ventral axis was characterized by higher connectivity with domain-general control networks on one hand (dorsal LIFG), and with the semantic network, on the other (ventral). These results provide novel insights into a graded functional organisation of the LIFG underpinning both task-free and task-constrained mental states, and suggest that the LIFG is an interface between distinct large-scale functional networks.

Significance statement

To understand how function varies across the LIFG, we conducted a detailed, bimodal exploration of the spatial transitions in its voxel-wise FC patterns. We provide novel evidence of graded changes along two main organisational axes. Specifically, the LIFG was characterized by an anterior-posterior gradient, which could reflect a shift in function from perceptually-driven processing to task-oriented control processes. Moreover, we revealed a dorsal-ventral shift in FC that is consistent with the idea that domain-specificity is a core principle underpinning functional organisation of the LIFG. These gradients were replicated across task-free and task-constrained FC measures, suggesting that a similar fundamental organisation underpins both mental states.
Genetically Defined Subtypes of Somatostatin-Containing Cortical Interneurons
Authors: Hostetler Rachel E. , Hu Hang , Agmon Ariel
Published: February 2023

Inhibitory interneurons play a crucial role in proper development and function of the mammalian cerebral cortex. Of the different inhibitory subclasses, dendritic-targeting, somatostatin-containing (SOM) interneurons may be the most diverse. Earlier studies used transgenic mouse lines to identify and characterize subtypes of SOM interneurons by morphological, electrophysiological and neurochemical properties. More recently, large-scale studies classified SOM interneurons into 13 morpho-electro-transcriptomic (MET) types. It remains unclear, however, how these various classification schemes relate to each other, and experimental access to MET types has been limited by the scarcity of type-specific mouse driver lines. To begin to address these issues we crossed Flp and Cre driver mouse lines and a dual-color combinatorial reporter, allowing experimental access to genetically defined SOM subsets. Brains from adult mice of both sexes were retrogradely dye-labeled from the pial surface to identify layer 1-projecting neurons, and immunostained against several marker proteins, allowing correlation of genetic label, axonal target and marker protein expression in the same neurons. Using whole-cell recordings ex-vivo, we compared electrophysiological properties between intersectional and transgenic SOM subsets. We identified two layer 1-targeting intersectional subsets with non-overlapping marker protein expression and electrophysiological properties which, together with a previously characterized layer 4-targeting subtype, account for about half of all layer 5 SOM cells and >40% of all SOM cells, and appear to map onto 5 of the 13 MET types. Genetic access to these subtypes will allow researchers to determine their synaptic inputs and outputs and uncover their roles in cortical computations and animal behavior.

SIGNIFICANCE STATEMENT

Inhibitory neurons are critically important for proper development and function of the cerebral cortex. Although a minority population, they are highly diverse, which poses a major challenge to investigating their contributions to cortical computations and animal and human behavior. As a step towards understanding this diversity we crossed genetically modified mouse lines to allow detailed examination of genetically-defined groups of the most diverse inhibitory subtype, somatostatin-containing interneurons. We identified and characterized three somatostatin subtypes in the deep cortical layers with distinct combinations of anatomical, neurochemical and electrophysiological properties. Future studies could now use these genetic tools to examine how these different subtypes are integrated into the cortical circuit and what roles they play during sensory, cognitive or motor behavior.