bluuebunny/crossref_metadata_2025 huggingface dataset:
California’s forest carbon offsets buffer pool is severely undercapitalized
Authors: Badgley Grayson , Chay Freya , Chegwidden Oriana S. , Hamman Joseph J. , Freeman Jeremy , Cullenward Danny
Published: May 2022

California operates a large forest carbon offsets program that credits carbon stored in forests across the continental United States and parts of coastal Alaska. These credits can be sold to buyers who wish to justify ongoing emissions, including in California’s cap-and-trade program. Although fossil CO2 emissions have effectively permanent atmospheric consequences, carbon stored in forests is inherently less durable because forests are subject to significant socioeconomic and physical risks that can cause temporarily stored carbon to be re-released into the atmosphere. To address these risks, California’s program is nominally designed to provide a 100-year guarantee on forest carbon claims based on a self-insurance program known as a buffer pool. Projects contribute credits to the buffer pool based on a suite of project-specific risk factors, with buffer pool credits retired as needed to cover carbon losses from events such as wildfire or drought. So long as the buffer pool remains solvent, the program’s permanence claim remains intact. Here, we perform an actuarial analysis of the performance of California’s buffer pool. We document how wildfires have depleted nearly one-fifth of the total buffer pool in less than a decade, equivalent to at least 95 percent of the program-wide contribution intended to manage all fire risks for 100 years. We also show that potential carbon losses from a single forest disease, sudden oak death, could fully encumber all credits set aside for disease and insect risks. These findings indicate that California’s buffer pool is severely undercapitalized and therefore unlikely to be able to guarantee the environmental integrity of California’s forest offsets program for 100 years.
Interphotoreceptor matrix proteoglycans IMPG1 and IMPG2 proteolyze in the SEA domain and reveal localization mutual dependency
Authors: Mitchell Benjamin , Coulter Chloe , Geldenhuys Werner J. , Rhodes Scott , Salido Ezequiel M.
Published: May 2022

The interphotoreceptor matrix (IPM) is a specialized extracellular mesh of molecules surrounding the inner and outer segments of photoreceptor neurons. Interphotoreceptor matrix proteoglycan 1 and 2 (IMPG1 and IMPG2) are major components of the IPM. Both proteoglycans possess SEA (sperm protein, enterokinase and agrin) domains, which may support proteolysis. Interestingly mutations in the SEA domains of IMPG1 and IMPG2 are associated with vision disease in humans. However, if SEA domains in IMPG molecules undergo proteolysis, and how this contributes to vision pathology is unknown. Therefore, we investigated SEA-mediated proteolysis of IMPG1 and IMPG2 and its significance to IPM physiology. Immunoblot analysis confirmed proteolysis of IMPG1 and IMPG2 in the retinas of wildtype mice. Point mutations mimicking human mutations in the SEA domain of IMPG1 that are associated with vision disease inhibited proteolysis. These findings demonstrate that proteolysis is part of the maturation of IMPG1 and IMPG2, in which deficits are associated with vision diseases. Further, immunohistochemical assays showed that proteolysis of IMPG2 generated two subunits, a membrane-attached peptide and an extracellular peptide. Notably, the extracellular portion of IMPG2 trafficked from the IPM around the inner segment toward the outer segment IPM by an IMPG1-dependent mechanism. This result provides the first evidence of a trafficking system that shuttles IMPG1 and IMPG2 from the inner to outer IPM in a co-dependent manner. In addition, these results suggest an interaction between IMPG1–IMPG2, and propose that mutations affecting one IMPG could affect the localization of the normal IMPG partner contributing to the disease mechanism of vision diseases associated with defective IMPG molecules.
A translational MRI approach to validate acute axonal damage detection
Authors: Toschi Nicola , Cerdá Antonio Cerdán , Treaba Constantina A , Barletta Valeria , Herranz Elena , Mehndiratta Ambica , Mainero Caterina , De Santis Silvia
Published: May 2022

Axonal degeneration is a central pathological feature of neurodegenerative pathologies and is closely associated with irreversible clinical disability. Current noninvasive methods to detect axonal damage in vivo are limited in their specificity, clinical applicability, and lack of proper validation. We aimed to validate an MRI framework based on multicompartment modeling of the diffusion-weighted signal (AxCaliber) in rats in the presence of axonal pathology, achieved through injection of a neurotoxin damaging the neuronal terminal of axons. We then applied the same MRI protocol to map axonal integrity in the whole brain of multiple sclerosis relapsing-remitting patients and age-matched healthy controls, a pathology associated with a neurodegenerative component.

AxCaliber is sensitive to microstructural axonal damage in rats, as demonstrated by a significant increase in the mean axonal caliber along the target tract, which correlated with the neurotoxin neurofilament staining. In humans, we uncovered a diffuse increase in mean axonal caliber in multiple sclerosis lesions and, importantly, in most areas of the normal-appearing white matter. Our results demonstrate that axonal diameter mapping is a sensitive and specific imaging biomarker able to link noninvasive imaging contrasts with the underlying biological substrate, supporting the key role of generalized axonal damage useful in diseases such as multiple sclerosis.
Environmental DNA from archived leaves reveals widespread temporal turnover and biotic homogenization in forest arthropod communities
Authors: Krehenwinkel Henrik , Weber Sven , Broekmann Rieke , Melcher Anja , Hans Julian , Wolf Ruediger , Hochkirch Axel , Kennedy Susan Rachel , Koschorreck Jan , Kuenzel Sven , Müller Christoph , Retzlaff Rebecca , Teubner Diana , Schanzer Sonja , Klein Roland , Paulus Martin , Udelhoven Thomas , Veith Michael
Published: May 2022

A major limitation of current reports on insect declines is the lack of standardized, long-term, and taxonomically broad time series. Here, we demonstrate the utility of environmental DNA from archived leaf material to characterize plant-associated arthropod communities. We base our work on several multi-decadal leaf time series from tree canopies in four land use types, which were sampled as part of a long-term environmental monitoring program across Germany. Using these highly standardized and well-preserved samples, we analyze temporal changes in communities of several thousand arthropod species belonging to 23 orders using metabarcoding and quantitative PCR. Our data do not support widespread declines of α-diversity or genetic variation within sites. Instead, we find a gradual community turnover, which results in temporal and spatial biotic homogenization, across all land use types and all arthropod orders. Our results suggest that insect decline is more complex than mere α-diversity loss, but can be driven by β-diversity decay across space and time.
Centrally expressed Cav3.2 T-type calcium channel is critical for the initiation and maintenance of neuropathic pain
Authors: Fayad Sophie L. , Ourties Guillaume , Le Gac Benjamin , Jouffre Baptiste , Lamoine Sylvain , Fruquière Antoine , Laffray Sophie , Gasmi Laila , Cauli Bruno , Mallet Christophe , Bourinet Emmanuel , Bessaih Thomas , Lambert Régis C. , Leresche Nathalie
Published: May 2022

Cav3.2 T-type calcium channel is a major molecular actor of neuropathic pain in peripheral sensory neurons, but its involvement at the supra-spinal level is almost unknown. In the Anterior Pretectum (APT), a hub of connectivity of the somatosensory system involved in pain perception, we show that Cav3.2 channels are expressed in a sub-population of GABAergic neurons co-expressing parvalbumin (PV). In these PV-expressing neurons, Cav3.2 channels contribute to a high frequency bursting activity, which is increased in the spared nerve injury model of neuropathy. Specific deletion of Cav3.2 channels in APT neurons reduced both the initiation and maintenance of mechanical and cold allodynia. These data are a direct demonstration that centrally expressed Cav3.2 channels also play a fundamental role in pain pathophysiology.
Phorbolester-activated Munc13-1 and ubMunc13-2 exert opposing effects on dense-core vesicle secretion
Authors: Houy Sébastien , Martins Joana S. , Lipstein Noa , Sørensen Jakob B.
Published: May 2022

Munc13 proteins are priming factors for SNARE-dependent exocytosis, which are activated by diacylglycerol (DAG)-binding to their C1-domain. Several Munc13 paralogs exist, but their differential roles are not well understood. We studied the interdependence of phorbolesters (DAG mimics) with Munc13-1 and ubMunc13-2 in mouse adrenal chromaffin cells. Although expression of either Munc13-1 or ubMunc13-2 stimulated secretion, phorbolester was only stimulatory for secretion when ubMunc13-2 expression dominated, but inhibitory when Munc13-1 dominated. Accordingly, phorbolester stimulated secretion in wildtype cells, or cells overexpressing ubMunc13-2, but inhibited secretion in Munc13-2/Unc13b knockout (KO) cells or in cells overexpressing Munc13-1. Phorbolester was more stimulatory in the Munc13-1/Unc13a KO than in WT littermates, showing that endogenous Munc13-1 limits the effects of phorbolester. Imaging showed that ubMunc13-2, but not Munc13-1, traffics to the plasma membrane with a time-course matching Ca2+-dependent secretion, and trafficking is independent of synaptotagmin-7 (syt7). However, in the absence of syt7, phorbolester became inhibitory for both Munc13-1 and ubMunc13-2 driven secretion, indicating that stimulatory phorbolester x Munc13-2 interaction depends obligatorily on functional pairing with syt7. Overall, DAG/phorbolester, ubMunc13-2 and syt7 form a stimulatory triad for dense-core vesicle priming.
Quality Control Framework of TCM Preparations based on Multi-type Fingerprints using a Source Proportion Estimation Model
Authors: Zha Yuguo , Yao Qi , Zhao Dan , Zhu Xue , Bai Hong , Ning Kang
Published: May 2022

Traditional Chinese Medicine (TCM) preparations have been widely used in clinical practice for the treatment of various diseases. The quality of TCM preparations is related to clinical efficacy and safety and is highly valued by researchers. The authenticity of TCM preparation can be guaranteed objectively by accurate quality control according to the composition. Here, we proposed a quality control framework of TCM preparations, which is based on multi-type fingerprints using the source proportion estimation model (SPEM). The high-performance liquid chromatography (HPLC) analysis and the high-throughput sequencing analysis are employed to acquire the chemical and taxonomic fingerprints of samples, respectively. The quality of TCM preparations among different manufacturers or batches is evaluated by using SPEM, which is an unsupervised method for source identification of TCM samples. Results showed the good performance of the quality control framework, for example, SPEM achieved a mean accuracy of 0.778 based on the ITS2 taxonomic fingerprint when differentiating manufacturer of BazhenYimu Wan pill. Applications of the quality control framework revealed the batch effect in TCM samples, and environmental factors, such as geography have a profound impact on the consistency of TCM preparations. In summary, this study is an exploration in the field of digital development of TCM preparations and provide a new insight to quantify the batch effect among different batches of TCM samples.
Understanding Definitions and Reporting of Deaths Attributed to COVID-19 in the UK – Evidence from FOI Requests
Authors: Jefferson Tom , Dietrich Madeleine , Brassey Jon , Heneghan Carl
Published: May 2022

Death is a widely used outcome to assess the severity of pandemics. Accuracy in assigning the cause of death is of vital importance to define the impact of the agent, monitor its evolution, and compare its threat with those of other agents. Throughout the COVID-19 pandemic, there has been widespread reporting of aggregate death data with little attention paid to the accuracy of the assignment of causation.

We aimed to analyse public authorities’ understanding of the assignment of cause of deaths during the SARS-CoV-2 pandemic in the UK by accessing Freedom of Information requests posed in three periods in 2020-21. By public authorities, we mean NHS Health Trusts, laboratories, and government agencies such as Public Health England and the Department of Health and Social Care. We searched WhatDoTheyKnow using the terms “covid and death”. We excluded those requests to bodies that cannot provide an answer (e.g. Councils) and those dealing with the effects of vaccines.

We grouped questions into themes addressing the definitions and causes of death relevant to the pandemic. We looked at the responses to the questions of the definition of cause of death, the accuracy of the attribution, the role of other pre-existing pathologies and how these were reported and quantified.

We found 800 requests from over 90 individuals. There was no consistency in the definition of cause of death or contributory cause of death across national bodies and in different bodies within the same nation. Nursing home providers, as well as medical practitioners, can assign a cause of death according to the Care Quality Commission. Post-mortem examinations were uncommon, the ONS did not incorporate their results in the summary of deaths by cause during the pandemic period. The meaning of the words “test” or “swab” was never clarified by any of the respondents. In care homes in England 1,304 out of 17,264 COVID-19 (7.6%, range 0% to 63%) mentioned COVID-19 in the absence of contributory or other factors in the death certificate, making it impossible to ascertain a chain of causality. The inconsistencies already noted hinder the ascertainment of the role of each factor leading to death and the quantification of the importance of infection. Some responses indicate that SARS-CoV-2 negative individuals or those whose death was not caused by COVID-19 were classified as “COVID-19 deaths”. We found 14 different ways of attributing the causes of death mentioned by respondents.

The overall lack of consistency has confused the public and likely led to erroneous conclusions. We are unable to separate the effects on deaths of SARS-CoV-2 from those of human interventions. A coherent process based on consistent definitions across the devolved nations is required. Furthermore, to enhance the accuracy of causation in pandemics a subset of deaths should be verified using autopsies with full medical documentation.
Molecular architecture of the autoinhibited kinesin-1 lambda particle
Authors: Weijman Johannes F. , Yadav Sathish K.N. , Surridge Katherine J. , Cross Jessica A. , Borucu Ufuk , Mantell Judith , Woolfson Derek N. , Schaffitzel Christiane , Dodding Mark P.
Published: May 2022

Despite continuing progress in kinesin enzyme mechanochemistry and emerging understanding of the cargo recognition machinery, it is not known how these functions are coupled and controlled by the alpha-helical coiled coils encoded by a large component of kinesin protein sequences. Here, we combine computational structure prediction with single-particle negative stain electron microscopy to reveal the coiled-coil architecture of heterotetrameric kinesin-1, in its compact state. An unusual flexion in the scaffold enables folding of the complex, bringing the kinesin heavy chain-light chain interface into close apposition with a tetrameric assembly formed from the region of the molecule previously assumed to be the folding hinge. This framework for autoinhibition is required to uncover how engagement of cargo and other regulatory factors drive kinesin-1 activation.

Summary statement

Integration of computational structure prediction with electron microscopy reveals the coiled-coil architecture of the autoinhibited compact conformer of the microtubule motor, kinesin-1.
Long-term temporal trends in gastrointestinal parasite infection in wild Soay sheep
Authors: Hayward Adam D. , Behnke Jerzy M. , Childs Dylan Z. , Corripio-Miyar Yolanda , Fenton Andy , Fraser Mariecia D. , Kenyon Fiona , McNeilly Tom N. , Pakeman Robin J. , Pedersen Amy B. , Pemberton Josephine M. , Sweeny Amy R. , Wilson Ken , Pilkington Jill G.
Published: May 2022

Monitoring the prevalence and abundance of parasites over time is important for addressing their potential impact on host life-histories, immunological profiles, and their influence as a selective force. Only long-term ecological studies have the potential to shed light on both the temporal trends in infection prevalence and abundance and the drivers of such trends, because of their ability to dissect drivers that may be confounded over shorter time scales. Despite this, only a relatively small number of such studies exist. Here, we analysed changes in the prevalence and abundance of gastrointestinal parasites in the wild Soay sheep population of St Kilda across 31 years. The host population density has increased across the study, and population density is known to increase parasite transmission, but we found that density and year explained temporal variation in parasite prevalence and abundance independently. Prevalence of both strongyle nematodes and coccidian microparasites increased during the study, and this effect varied between lambs, yearlings and adults. Meanwhile, abundance of strongyles was more strongly linked to host density than to temporal (yearly) dynamics, while abundance of coccidia showed a strong temporal trend without any influence of density. Strikingly, coccidian abundance increased threefold across the course of the study in lambs, while increases in yearlings and adults were negligible. Our decades-long, intensive, individual-based study will enable the role of environmental change and selection pressures in driving these dynamics to be determined, potentially providing unparalleled insight into the drivers of temporal variation in parasite dynamics in the wild.

Key findings

We studied temporal trends in gastrointestinal parasites of wild sheep over 31 years

Year and host population density explained temporal variation in parasites independently

Prevalence of both strongyle nematodes and coccidia varied across the study period

Abundance of strongyles was more closely linked to host density than year

Abundance of coccidia increased threefold over time in lambs, but did not vary in adults
Distributed and gradual microstructure changes track the emergence of behavioural benefit from memory reactivation
Authors: Rakowska Martyna , Lazari Alberto , Cercignani Mara , Bagrowska Paulina , Johansen-Berg Heidi , Lewis Penelope A.
Published: May 2022

Memory traces develop gradually and link to neural plasticity. Memory reactivation during sleep is crucial for consolidation, but its precise impact on plasticity and contribution to long-term memory storage remains unclear. We used multimodal diffusion-weighted imaging to track the location and timescale of microstructural changes following Targeted Memory Reactivation (TMR) of a motor task. This showed continuous microstructure plasticity in precuneus across 10 days post-TMR, paralleling the gradual development of behavioural benefit. Both early (0 - 24 h post-TMR) and late (24 h - 10 days post-TMR) microstructural changes in striatum and sensorimotor cortex were associated with the emergence of behavioural effects of TMR at day 20. Furthermore, the baseline microstructural architecture of sensorimotor cortex predicted TMR susceptibility. These findings demonstrate that repeated reactivation of memory traces during sleep engenders microstructural plasticity which continues days after the stimulation night and is associated with the emergence of memory benefits at the behavioural level.
Argon plasma-modified bacterial cellulose filters for protection against respiratory pathogens
Authors: Żywicka Anna , Ciecholewska-Juśko Daria , Szymańska Magdalena , Drozd Radosław , Sobolewski Peter , Junka Adam , Gorgieva Selestina , El Fray Miroslawa , Fijałkowski Karol
Published: May 2022

Due to the global spread of the SARS-CoV-2 virus and the resultant pandemic, there has been a major surge in the demand for surgical masks, respirators, and other air filtration devices. Unfortunately, the fact that these filters are made of petrochemical-derived, non-biodegradable polymers means that the surge in production has also led to a surge in plastic waste. In this work, we present novel, sustainable filters based on bacterial cellulose (BC) functionalized with low-pressure argon plasma (LPP-Ar). The “green” production process involved BC biosynthesis by Komagataeibacter xylinus, followed by simple purification, homogenization, lyophilization, and finally LPP-Ar treatment. The obtained LPP-Ar-functionalized BC-based material (LPP-Ar-BC-bM) showed excellent antimicrobial and antiviral properties, with no cytotoxicity versus murine fibroblasts in vitro. Further, filters consisting of three layers of LPP-Ar-BC-bM had >99% bacterial and viral filtration efficiency, while maintaining sufficiently low airflow resistance (6 mbar at an airflow of 95 L/min). Finally, as a proof-of-concept, we were able to prepare 80 masks with LPP-Ar-BC-bM filter and ~85% of volunteer medical staff assessed them as good or very good in terms of comfort. We conclude that our novel sustainable, biobased, biodegradable filters are suitable for respiratory personal protective equipment (PPE), such as surgical masks and respirators. Further, with scale-up, they may be adapted for indoor air handling filtration in hospitals or schools.

Graphical abstract
Analysis of allelic cross-reactivity of monoclonal IgG antibodies by a multiplexed reverse FluoroSpot assay
Authors: Hoffmann-Veltung Henriette , Anabire Nsoh Godwin , Ofori Michael Fokuo , Janhmatz Peter , Ahlborg Niklas , Hviid Lars , Quintana Maria del Pilar
Published: May 2022

The issue of antibody cross-reactivity is of central importance in immunology, and not least in protective immunity to Plasmodium falciparum malaria, where key antigens show substantial allelic variation (polymorphism). However, serological analysis often does not allow the distinction between true cross-reactivity (one antibody recognizing multiple antigen variants) and apparent cross-reactivity (presence of multiple variant-specific antibodies), as it requires analysis at the single B-cell/monoclonal antibody level. ELISpot is an assay that enables that, and a recently developed multiplexed variant of ELISpot (FluoroSpot) facilitates simultaneous assessment of B-cell/antibody reactivity to several different antigens. In this study, we present a further enhancement of this assay that makes direct analysis of monoclonal antibody-level cross-reactivity with allelic variants feasible. Using VAR2CSA-type PfEMP1 – a notoriously polymorphic antigen involved in the pathogenesis of placental malaria – as a model, we demonstrate the robustness of the assay and its applicability to analysis of true cross-reactivity of monoclonal VAR2CSA-specific antibodies in naturally exposed individuals. The assay is adaptable to the analysis of other polymorphic antigens, rendering it a powerful tool in studies of immunity to malaria and many other diseases.
Pericyte remodeling is deficient in the aged brain and contributes to impaired capillary flow and structure
Authors: Berthiaume Andrée-Anne , Schmid Franca , Stamenkovic Stefan , Coelho-Santos Vanessa , Nielson Cara D. , Weber Bruno , Majesky Mark W. , Shih Andy Y.
Published: May 2022

Deterioration of brain capillary flow and architecture is a hallmark of aging and dementia. It remains unclear how loss of brain pericytes in these conditions contributes to capillary dysfunction. Here, we conduct cause-and-effect studies by optically ablating pericytes in adult and aged mice in vivo. Focal pericyte loss induces capillary dilation without blood-brain barrier disruption. These abnormal dilations are exacerbated in the aged brain, and result in increased flow heterogeneity in capillary networks. A subset of affected capillaries experience reduced perfusion due to flow steal. Some capillaries stall in flow and regress, leading to loss of capillary connectivity. Remodeling of neighboring pericytes restores endothelial coverage and vascular tone within days. Pericyte remodeling is slower in the aged brain, resulting in regions of persistent capillary dilation. These findings link pericyte loss to disruption of capillary flow and structure. They also identify pericyte remodeling as a therapeutic target to preserve capillary flow dynamics.
Focus-ISM for Sharp and Gentle Super-Resolved Microscopy
Authors: Tortarolo Giorgio , Zunino Alessandro , Fersini Francesco , Castello Marco , Piazza Simonluca , Sheppard Colin J.R. , Bianchini Paolo , Diaspro Alberto , Koho Sami , Vicidomini Giuseppe
Published: May 2022

Super-resolution microscopy is routinely used for fixed and thin samples, while its feasibility for imaging live and thick samples is still limited. In the case of stimulated emission depletion (STED) microscopy, the high-intensity illumination required to achieve effective sub-diffraction resolution can introduce photo-damage, thus reducing the compatibility of the technique with live-cell imaging. Moreover, the out-of-focus fluorescence background may overcome the often faint signal stemming from the focal point, thus constraining imaging to thin samples. Here, we combined STED microscopy with image-scanning microscopy (ISM) to mitigate these limitations without any practical disadvantages. We first enhanced a laser scanning microscope (LSM) by introducing a detector array, hence providing access to a set of additional spatial information that is not available with a typical single-element detector. Then, we exploited this extended dataset to implement focus-ISM, a novel method that relaxes the high-intensity requirement of STED microscopy and removes the out-of-focus background. Additionally, we generalized the focus-ISM method to conventional LSM, namely without a STED beam. The proposed approach requires minimal architectural changes compared with conventional STED microscopes but provides substantial advantages for live and thick sample imaging while maintaining all compatibility with all recent advances in STED and confocal microscopy. As such, focus-ISM represents an essential step towards a universal super-resolved LSM technique for subcellular imaging.
PILS proteins provide a homeostatic feedback on auxin signaling output
Authors: Feraru Elena , Feraru Mugurel I. , Moulinier-Anzola Jeanette , Schwihla Maximilian , Ferreira Da Silva Santos Jonathan , Sun Lin , Waidmann Sascha , Korbei Barbara , Kleine-Vehn Jürgen
Published: May 2022

Auxin is a crucial regulator of plant growth and development. Multiple internal and external signals converge at the regulation of auxin metabolism, intercellular transport, and signaling (Pernisova and Vernoux, 2021; Anfang and Shani, 2021). Considering this complexity, it remains largely unknown how plant cells monitor and ensure the homeostasis of auxin responses. PIN-LIKES (PILS) intracellular auxin transport facilitators at the endoplasmic reticulum (ER) are suitable candidates to buffer cellular auxin responses, because they limit nuclear abundance and signaling of auxin (Barbez et al., 2012; Beziat et al., 2017; Feraru et al., 2019; Sun et al., 2020). We used forward genetics to identify mechanisms that define the PILS6 protein abundance and thereby auxin signaling outputs. We screened for gloomy and shiny pils (gasp) mutants that define the levels of PILS6-GFP under a constitutive promoter. In this study, we show that GASP1 encodes for an uncharacterized RING/U-box superfamily protein and impacts on auxin signaling output. We conclude that the low auxin signaling in gasp1 mutants correlates with reduced abundance of PILS proteins, such as PILS5 and PILS6, which consequently balances auxin-related phenotypes. In agreement, we show that high and low auxin conditions increase and reduce PILS6 protein levels, respectively. Accordingly, non-optimum auxin concentrations are buffered by alterations in PILS6 abundance, consequently leading to homeostatic auxin output regulation. We envision that this feedback mechanism provides robustness to auxin-dependent plant development.
Genomic analyses identify significant biological processes in DDX21-mediated colorectal cancer cells
Authors: Wang Xueying , Zhang Donghong , Wang Mengshan
Published: May 2022

Colorectal cancer is the third most common cancer in the US. There has been an incline in the number of young patients with colorectal cancer due to unclear reasons at this point in time. Currently, DEAD-box RNA helicase protein DDX21 is identified as a prognosis marker for early-stage colorectal cancer. However, the mechanism of DDX21 mediated-colorectal cancer is still unknown. Here, our objective is to determine the key molecules and signaling by analyzing the RNA-seq data. The GSE184726 was created by the Illumina NovaSeq 6000 (Homo sapiens). The KEGG and GO analyses indicated Neuroactive ligand−receptor interaction and Ras signaling pathway were the key signaling pathways during the knockdown of DDX21 in colorectal cancer. Moreover, we identified several interactive genes including PTPRC, FN1, ITGAM, RAD51, TRAF6, CCNB1, FOXP3, CCNA2, HIST2H2AC, and HSPA5. Our study may provide new insights into the treatment of colorectal cancer.
Dispersal between interconnected patches can reduce the total population size
Authors: Vortkamp Irina , Kost Christian , Hermann Marita , Hilker Frank M.
Published: May 2022

Human activities increasingly result in a fragmentation of natural ecosystems. However, the ecological consequences of fragmentation remain poorly understood. While some studies report that fragmentation may enhance population growth, others suggest the opposite pattern. Here we investigated how habitat connectivity affects the population size of a single species when habitat patches differ in quality. We combined dispersal experiments, in which bacterial populations of Escherichia coli were repeatedly transferred between two qualitatively different environments, with a process-based mathematical model. Both experiments and model consistently revealed that increased dispersal between patches reduced the total population size, thus demonstrating a detrimental effect of habitat connectivity on population size. This observation could be explained with a net loss of individuals upon migration from a productive to an overcrowded patch. Our findings suggest that conservation measures, which promote movement between fragmented habitats, such as dispersal corridors or stepping stones, are potentially detrimental for some species.
Matrix obstructions cause multiscale disruption in collective epithelial migration by suppressing physical function of leader cells
Authors: Lee Ye Lim , Mathur Jairaj , Walter Christopher , Zmuda Hannah , Pathak Amit
Published: May 2022

Cellular forces and intercellular cooperation generate collective cell migration. Pathological changes in cell-level genetic and physical properties cause jamming, unjamming, and scattering in epithelial migration. Separately, changes in microenvironment stiffness and confinement can produce varying modes of cell migration. However, it remains unclear whether and how mesoscale disruptions in matrix topology alter collective cell migration. To address this question, we microfabricated matrices with stumps of defined geometry, density, and orientation, which serve as obstructions in the path of collectively migrating healthy mammary epithelial cells. Here, we show that cells lose their speed and directionality when moving through dense obstructions, compared to those sparsely spaced. On flat surfaces, leader cells are significantly stiffer than follower cells, while dense obstructions lead to the overall softening of cells. In moving through dense obstructions, epithelial cells lose the sense of leaders and followers in their physical properties, migration phenotypes, and fluidity. Although Rac inhibition reduces obstruction sensitivity, loss of cell-cell cooperation and induction of leader-like phenotype via α-catenin depletion eliminates the effect of matrix obstructions on epithelial migration. Through a lattice-based model, we identify cellular protrusions, polarity, and leader-follower communication as key mechanisms for obstruction-sensitive collective cell migration. Together, microscale cytoskeletal response, mesoscale softening and disorder, and macroscale multicellular communication enable epithelial cell populations to sense topological obstructions encountered in challenging environments. These results reveal that cohesive, healthy populations are more obstruction sensitive than the dysfunctional, aggressive ones. The ‘obstruction-sensitivity’ could add to the emerging disease ‘mechanotypes’ such as cell stiffness and traction forces.
MCIBox: A Toolkit for Single-molecule Multi-way Chromatin Interaction Visualization and Micro-Domains Identification
Authors: Tian Simon Zhongyuan , Li Guoliang , Ning Duo , Jing Kai , Xu Yewen , Yang Yang , Fullwood Melissa J. , Yin Pengfei , Huang Guangyu , Plewczynski Dariusz , Wang Wenxin , Zhai Jixian , Wang Ziying , Dai Ziwei , Lin Yuxin , Chen Wei , Zheng Meizhen
Published: May 2022

The emerging ligation-free three-dimensional (3D) genome mapping technologies can identify multiplex chromatin interactions with single-molecule precision. These technologies offer new insight into high-dimensional chromatin organization and gene regulation, but also introduce new challenges in data visualization and analysis. To overcome these challenges, we developed MCIBox, a toolkit for Multi-way Chromatin Interaction (MCI) analysis, including a visualization tool and a platform for identifying micro-domains with clustered single-molecule chromatin complexes. MCIBox is based on various clustering algorithms integrated with dimensionality reduction methods that can display multiplex chromatin interactions at single-molecule level, allowing users to explore chromatin extrusion patterns and super-enhancers regulation modes in transcription, and to identify single-molecule chromatin complexes that are clustered into micro-domains. Furthermore, MCIBox incorporates a two-dimensional kernel density estimation algorithm to identify micro-domains boundaries automatically. These micro-domains were stratified with distinctive signatures of transcription activity and contained different cell cycle associated genes. MCIBox could potentially distinguish the specificity of single-molecule chromatin interaction patterns in various phases of a cell cycle or cell types.
Adaptation of the eyes of grass puffer (Takifugu niphobles) to the riverine and marine environments
Authors: Osada Misa , Terai Yohey
Published: May 2022

Many marine fish species migrate to rivers, but little is known about whether these species switch their vision when inhabiting rivers or adapt their vision to the environment of both rivers and the sea. Grass puffer (Takifugu niphobles) is a marine fish species frequently migrating to rivers. In this study, we investigated grass puffers from riverine and marine populations and analyzed the gene expression in their eyes. The phylogeny and population genetics of riverine and marine grass puffers indicated that riverine and marine grass puffers are from the same population. Gene expression levels by high-throughput RNA sequencing indicated no differences in the expression patterns of vision-related genes in marine and riverine grass puffers. This result indicates that the adaption of their visual system to both marine and riverine environments rather than switching the expression of vision-related genes. Additionally, riverine grass puffers increase the expression levels of heat shock proteins and related genes. These genes showed higher expression in riverine grass puffer than in other marine and river pufferfish species, suggesting that the grass puffer individuals adapt to the environmental difference when they migrate to the river by increasing the expression levels of heat shock protein and related genes.
Experimental Guidance for Discovering Genetic Networks through Iterative Hypothesis Reduction on Time Series
Authors: Cummins Breschine , Motta Francis C. , Moseley Robert C. , Deckard Anastasia , Campione Sophia , Gedeon Tomáš , Mischaikow Konstantin , Haase Steven B.
Published: May 2022

Large programs of dynamic gene expression, like cell cyles and circadian rhythms, are controlled by a relatively small “core” network of transcription factors and post-translational modifiers, working in concerted mutual regulation. Recent work suggests that system-independent, quantitative features of the dynamics of gene expression can be used to identify core regulators. We introduce an approach of iterative network hypothesis reduction from time-series data in which increasingly complex features of the dynamic expression of individual, pairs, and entire collections of genes are used to infer functional network models that can produce the observed transcriptional program. The culmination of our work is a computational pipeline, Iterative Network Hypothesis Reduction from Temporal Dynamics (Inherent Dynamics Pipeline), that provides a priority listing of targets for genetic perturbation to experimentally infer network structure. We demonstrate the capability of this integrated computational pipeline on synthetic and yeast cell-cycle data.

Author Summary

In this work we discuss a method for identifying promising experimental targets for genetic network inference by leveraging different features of time series gene expression data along a chained set of previously published software tools. We aim to locate small networks that control oscillations in the genome-wide expression profile in biological functions such as the circadian rhythm and the cell cycle. We infer the most promising targets for further experimentation, emphasizing that modeling and experimentation are an∗Corresponding author: breschine.cummins@montana.edu essential feedback loop for confident predictions of core network structure. Our major offering is the reduction of experimental time and expense by providing targeted guidance from computational methods for the inference of oscillating core networks, particularly in novel organisms.
Independent Replication and Drug-specificity of an Antidepressant Response Polygenic Risk Score
Authors: Lin Bochao , Arns Martijn , Rutten Bart , Gordon Evian , Luykx Jurjen J.
Published: May 2022

We here examine associations of a recently published polygenic risk score of antidepressant response (PRS-AR) with antidepressant treatment outcomes (remission and depression score change) in an independent clinical trial. We not only replicate the PRS-AR for escitalopram, but also find antidepressant interaction effects, suggesting drug-specificity of PRS-AR. We therefore also tested the utility of this PRS-AR to stratify between antidepressants and demonstrate a 14% increase in remission rate (from 43.6% to 49.7%), relative to the randomized remission rate.
Genetically determining individualized clinical reference ranges for the biomarker tryptase can limit unnecessary procedures and unmask myeloid neoplasms
Authors: Chovanec Jack , Tunc Ilker , Hughes Jason , Halstead Joseph , Mateja Allyson , Liu Yihui , O’Connell Michael P. , Kim Jiwon , Park Young Hwan , Wang Qinlu , Le Quang , Pirooznia Mehdi , Trivedi Neil N. , Bai Yun , Yin Yuzhi , Hsu Amy P. , McElwee Josh , Lassiter Sheryce , Nelson Celeste , Bandoh Judy , DiMaggio Thomas , Šelb Julij , Rijavec Matija , Carter Melody C. , Komarow Hirsh D. , Sabato Vito , Steinberg Joshua , Hafer Kurt M. , Feuille Elizabeth , Hourigan Christopher S. , Lack Justin , Khoury Paneez , Maric Irina , Zanotti Roberta , Bonadonna Patrizia , Schwartz Lawrence B. , Milner Joshua D. , Glover Sarah C. , Ebo Didier G. , Korošec Peter , Caughey George H. , Brittain. Erica H. , Busby Ben , Metcalfe Dean D. , Lyons Jonathan J.
Published: May 2022

Serum tryptase is a biomarker used to aid in the identification of certain myeloid neoplasms, most notably systemic mastocytosis, where baseline (BST) levels >20 ng/mL are a minor criterion for diagnosis. Whereas clonal myeloid neoplasms are rare, the common cause for elevated BST is the genetic trait hereditary alpha-tryptasemia (HαT) caused by increased germline TPSAB1 copy number. To date, the precise structural variation and mechanism(s) underlying elevated BST in HαT and the general clinical utility of tryptase genotyping, remain undefined. Through cloning, long-read sequencing, and assembling of the human tryptase locus from an individual with HαT, and validating our findings in vitro and in silico, we demonstrate that BST elevations arise from over-expression of replicated TPSAB1 loci encoding wild-type α-tryptase due to co-inheritance of a linked over-active promoter element. Modeling BST levels based upon TPSAB1 replication number we generate new individualized clinical reference values for the upper limit of ‘normal’. Using this personalized laboratory medicine approach, we demonstrate the clinical utility of tryptase genotyping, finding that in the absence of HαT, BST levels >11.4 ng/mL frequently identify indolent clonal mast cell disease. Moreover, substantial BST elevations (e.g., >100 ng/mL) which would ordinarily prompt bone marrow biopsy, can result from TPSAB1 replications alone and thus be within ‘normal’ limits for certain individuals with HαT.
Therapeutic effects of PTCD and ERCP in patients with obstructive severe acute biliary pancreatitis
Authors: Zhang Xue Ling , Sun Jia Huan , Wu Yue , Xie Min , Li Cong Cong , Lv Dong , Yu Wei , Cui Pei Lin
Published: May 2022

Objective

We evaluated the therapeutic effects of PTCD and ERCP in patients with obstructive severe acute biliary pancreatitis (SABP).

Methods

A total of 62 patients with obstructive SABP were enrolled in this study from July 2013 to July 2019 and divided into three groups: PTCD group (n=22), ERCP group (n=24) and conservative group (n=16). Based on treatment time, PTCD and ERCP groups were further separated into early (⩽ 72 h) and delayed (>72 h) groups. Laboratory indices, hospitalization days, recovery of liver functions and remission of abdominal pain as well as complications were evaluated to establish the efficacy and suitable time.

Results

The average hospitalization days, time for abdominal pain relief and laboratory indices (leukocyte, blood amylase, ALT and TBiL) recovery were shorter (p<0.05) in PTCD and ERCP groups. The average hospitalization days for the ERCP group (16.71±3.99) were shorter, compared to the PTCD group (19.64±4.27) (p<0.05). Complications were few in ERCP (33.33%) and PTCD (27.27%) groups. The average length of stay (13.88±3.27), recovery time of leukocyte (6.31±0.92) and TBiL (9.13±1.98) in the early ERCP group were shorter than in both delayed ERCP and early PTCD groups (p<0.05). The average length of stay (18.63±4.06) and ALT recovery time (12.25±2.59) in delayed ERCP group were shorter than in delayed PTCD group (p<0.05).

Conclusions

Both ERCP and PTCD are effective for relieving biliary obstruction during SABP, and early ERCP or PTCD within 72 h for obstructive SABP are more beneficial.
H4K16ac activates the transcription of transposable elements and contributes to their cis-regulatory function
Authors: Pal Debosree , Patel Manthan , Boulet Fanny , Sundarraj Jayakumar , Grant Olivia A , Branco Miguel R. , Basu Srinjan , Santos Silvia , Zabet Nicolae Radu , Scaffidi Paola , Pradeepa Madapura M
Published: May 2022

Mammalian genomes harbour a large number of transposable elements (TEs) and their remnants. Many epigenetic repression mechanisms are known to silence TE transcription. However, TEs are upregulated during early development, neuronal lineage, and cancers, although the epigenetic factors contributing to the transcription of TEs have yet to be fully elucidated. Here we demonstrated that the male-specific lethal (MSL) complex mediated acetylation of histone H4 lysine 16 (H4K16ac) activates transcription of long interspersed nuclear elements (LINE1, L1) and long terminal repeats (LTRs). Furthermore, we show that the H4K16ac marked L1 and LTR subfamilies function as enhancers and are enriched with chromatin features associated with active enhancers and looping factors. L1 and LTRs enriched with histone acetylations are bound by chromatin looping factors and these regions loop with genes. CRISPR-based epigenetic perturbation and genetic deletion of L1s reveal that H4K16ac marked L1s and LTRs regulate the expression of genes in cis. Overall, TEs enriched with H4K16ac contribute to the cis-regulatory landscape of a significant portion of the mammalian genome by maintaining an active chromatin landscape at TEs.

One Sentence Summary

H4K16ac activates LINE1 and ERV/LTR transcription and rewires the cis-regulatory landscape of a significant portion of the mammalian genome by increasing the transcriptional activity at TEs.
Robustness of the autophagy pathway to somatic copy number losses
Authors: Polo Pierfrancesco , Gremke Niklas , Stiewe Thorsten , Wanzel Michael
Published: May 2022

Autophagy allows cells to temporarily tolerate energy stress by replenishing critical metabolites through self-digestion, thereby attenuating the cytotoxic effects of anticancer drugs that target tumor metabolism. Autophagy defects could therefore mark a metabolically vulnerable cancer state and open a therapeutic window. While mutations of autophagy genes (ATGs) are notably rare in cancer, haploinsufficiency network analyses across many cancers have shown that the autophagy pathway is frequently hit by somatic copy number losses of ATGs likeMAP1LC3B/ATG8F(LC3),BECN1/ATG6(Beclin-1), andATG10. Here, we used CRISPR/Cas9 technology to delete increasing numbers of copies of one or more of these ATGs in non-small cell lung cancer cells and examined the effects on sensitivity to compounds targeting aerobic glycolysis, a hallmark of cancer metabolism. Whereas complete knock-out of one ATG blocked autophagy and led to profound metabolic vulnerability, this was not the case for combinations of different non-homozygous deletions. In cancer patients, the effect of ATG copy number loss was blunted at the protein level and did not lead to accumulation of p62 as a sign of reduced autophagic flux. Thus, the autophagy pathway is shown to be markedly robust and resilient, even with concomitant copy number loss of key autophagy genes.