Browse Articles

Learning the language of antibody hypervariability

Protein language models (PLMs) have demonstrated impressive success in modeling proteins. However, general-purpose “foundational” PLMs have limited performance in modeling antibodies due to the latter’s hypervariable regions, which do not conform to the evolutionary conservation principles that such models rely on. In this study, we propose a transfer learning framework called Antibody Mutagenesis-Augmented Processing (AbMAP), which fine-tunes foundational models for antibody-sequence inputs by supervising on antibody structure and binding specificity examples. Our learned feature representations accurately predict mutational effects on antigen binding, paratope identification, and other key antibody properties. We experimentally validate AbMAP for antibody optimization by applying it to refine a set of antibodies that bind to a SARS-CoV-2 peptide, and obtain an 82% hit-rate and up to 22-fold increase in binding affinity. AbMAP also unlocks large-scale analyses of immune repertoires, revealing that B-cell receptor repertoires of individuals, while remarkably different in sequence, converge toward similar structural and functional coverage. Importantly, AbMAP’s transfer learning approach can be readily adapted to advances in foundational PLMs. We anticipate AbMAP will accelerate the efficient design and modeling of antibodies, expedite the discovery of antibody-based therapeutics, and deepen our understanding of humoral immunity.

Muon spectroscopy of a 12-phosphatetraphene with extremely efficient radical trapping properties

A minimal vertex model explains how the amnioserosa avoids fluidization during <i>Drosophila</i> dorsal closure

Dorsal closure is a process that occurs during embryogenesis of Drosophila melanogaster . During dorsal closure, the amnioserosa (AS), a one-cell thick epithelial tissue that fills the dorsal opening, shrinks as the lateral epidermis sheets converge and eventually merge. During this process, both shape index and aspect ratio of amnioserosa cells increase markedly. The standard 2-dimensional vertex model, which successfully describes tissue sheet mechanics in multiple contexts, would in this case predict that the tissue should fluidize via cell neighbor changes. Surprisingly, however, the amnioserosa remains an elastic solid with no such events. We here present a minimal extension to the vertex model that explains how the amnioserosa can achieve this unexpected behavior. We show that continuous shrinkage of the preferred cell perimeter and cell perimeter polydispersity lead to the retention of the solid state of the amnioserosa. Our model accurately captures measured cell shape and orientation changes and predicts nonmonotonic junction tension that we confirm with laser ablation experiments.

Deep learning based approaches for intelligent industrial machinery health management and fault diagnosis in resource-constrained environments

Unveiling hidden reaction kinetics of carbon dioxide in supercritical aqueous solutions

Dissolution of CO 2 in water followed by the subsequent hydrolysis reactions is of great importance to the global carbon cycle, and carbon capture and storage. Despite numerous previous studies, the reactions are still not fully understood at the atomistic scale. Here, we combined ab initio molecular dynamics (AIMD) simulations with Markov state models to elucidate the reaction mechanisms and kinetics of CO 2 in supercritical water both in the bulk and nanoconfined states. The integration of unsupervised learning with first-principles data allows us to identify complex reaction coordinates and pathways automatically instead of a priori human speculation. Interestingly, our unbiased modeling found an unknown pathway of dissolving CO 2 (aq) under graphene nanoconfinement, involving the pyrocarbonate anion [C 2 O 5 2 − (aq)] as an intermediate state. The pyrocarbonate anion was previously hypothesized to have a fleeting existence in water; however, our study reveals that it is a crucial reaction intermediate and stable carbon species in the nanoconfined solutions. We even observed the formation of pyrocarbonic acid [H 2 C 2 O 5 (aq)], which was unknown in water, in our AIMD simulations. The unexpected appearance of pyrocarbonates is related to the superionic behavior of the confined solutions. We also found that carbonation reactions involve collective proton transfer along transient water wires, which exhibits concerted behavior in the bulk solution but proceeds stepwise under nanoconfinement. The first-principles Markov state models show substantial promise for elucidating complex reaction kinetics in aqueous solutions. Our study highlights the importance of large oxocarbons in aqueous carbon reactions, with great implications for the deep carbon cycle and the sequestration of CO 2 .

Enhanced particle swarm optimization with chaotic search for offshore micro-energy systems

Nonlinear excitation of energetic particle driven geodesic acoustic mode by resonance overlap with Alfvén instability in ASDEX Upgrade

Binding mode–guided development of high-performance antibodies targeting site-specific posttranslational modifications

Posttranslational modifications (PTMs) of proteins play critical roles in regulating many cellular events. Antibodies targeting site-specific PTMs are essential tools for detecting and enriching PTMs at sites of interest. However, fundamental difficulties in molecular recognition of both PTM and surrounding peptide sequence have hindered the efficient generation of highly sequence-specific anti-PTM antibodies. Furthermore, the widespread use of potentially inconsistent, nonrenewable, and molecularly undefined antibodies presents experimental challenges thought to contribute to the reproducibility problem in biomedical research. In this study, we describe the binding mode-guided development of a platform that efficiently generates potent and selective recombinant antibodies to PTMs that are molecularly defined and renewable. Our platform is built on our previous discovery of an unconventional binding mode of anti-PTM antibodies, antigen clasping, where two antigen binding sites cooperatively sandwich a single antigen, creating extensive interactions with the antigen and leading to high selectivity and potency. We designed the platform that generates clasping antibodies with two distinct binding units, resulting in efficient generation of antibodies to a set of trimethylated histone H3 with high levels of specificity and affinity. Performance comparison in chromatin immunoprecipitation, a common application in epigenomics, revealed that a clasping antibody to trimethylated histone H3 at lysine 27 exhibited superior specificity to a widely used conventional antibody and captured symmetric and asymmetric nucleosomes in a less biased manner. We further generated clasping antibodies to phosphotyrosine antigens by using the same principle. These results suggest the broad applicability of our platform to generating high-performance clasping antibodies to diverse PTMs.

Author Correction: JK-1, a useful erythroleukemic cell line model to study a controlled erythroid differentiation from progenitors to terminal erythropoiesis

ANAC044 orchestrates mitochondrial stress signaling to trigger iron-induced stem cell death in root meristems

While iron (Fe) is essential for life and plays important roles for almost all growth related processes, it can trigger cell death in both animals and plants. However, the underlying mechanisms for Fe-induced cell death in plants remain largely unknown. S-nitrosoglutathione reductase (GSNOR) has previously been reported to regulate nitric oxide homeostasis to prevent Fe-induced cell death within root meristems. Here, we found that in the absence of GSNOR , exposure to high Fe treatment results in DNA damage–dependent cell death specifically in vascular stem cells in root meristems within 48 h. Through a series of time-course transcriptomic analyses, we unveil that in the absence of GSNOR , mitochondrial dysfunction emerges as the most prominent response to high Fe treatment. Consistently, the application of mitochondrial respiratory inhibitors leads to stem cell death in root meristems, and pharmacological blockage of the voltage-dependent anion channel that is responsible for the release of mitochondrial-derived molecules into the cytosol or genetic changes that abolish the ANAC017- and ANAC013-mediated mitochondrial retrograde signaling effectively eliminate Fe-induced stem cell death in gsnor root meristems. We further identify the nuclear transcription factor ANAC044 as a mediator of this mitochondrial retrograde signaling. Disruption of ANAC044 completely abolishes the GSNOR-dependent, Fe-induced stem cell death in root meristems, while ectopic expression of ANAC044 causes severe root stem cell death. Collectively, our findings reveal a mechanism responsible for initiating Fe-induced stem cell death in the root meristem, which is the ANAC044-mediated GSNOR-regulated mitochondrial stress signaling pathway.

LEGO-Lipophosphonoxin membrane activity is enhanced by presence of phosphatidylethanolamine but hindered by outer membrane

Abstract Finding effective antibiotics against multi-resistant strains of bacteria has been a challenging race. Linker-Evolved-Group-Optimized-Lipophosphonoxins (LEGO-LPPOs) are small modular synthetic antibacterial compounds targeting the cytoplasmic membrane. Here we focused on understanding the reasons for the variable efficacy of selected LEGO-LPPOs ( LEGO-1 , LEGO-2 , LEGO-3 , and LEGO-4 ) differing in hydrophobic and linker module structure and length. LEGO-1–4 permeabilized cytoplasmic membrane of Staphylococcus aureus , Bacillus subtilis , Pseudomonas aeruginosa , and Escherichia coli , LEGO-1 with the longest linker module being the most effective. Gram-positive bacteria were more sensitive to LEGO-LPPO action compared to Gram-negatives, which was manifested as a delayed membrane permeabilization, higher minimal inhibitory concentration and lower amount of LEGO-LPPO bound to the cells. Outer membrane permeability measurements and time-kill assay showed that presence of the intact outer membrane brought about reduced susceptibility of Gram-negatives. Using liposome leakage and in silico simulations, we showed that membranes with major content of phosphatidylethanolamine were more prone to LEGO-LPPO permeabilization. The proposed mechanism stems from an electrostatic repulsion between highly positively charged LEGO-1 molecules and positively charged amino groups of phosphatidylethanolamine which destabilizes the membrane. Collectively, these data suggest that LEGO-LPPO membrane activity is enhanced by presence of phosphatidylethanolamine but hindered by presence of intact outer membrane.

VCP controls KCC2 degradation through FAF1 recruitment and accelerates emergence from anesthesia

Ubiquitin-proteasomal degradation of K + /Cl − cotransporter 2 (KCC2) in the ventral posteromedial nucleus (VPM) has been demonstrated to serve as a common mechanism by which the brain emerges from anesthesia and regains consciousness. Ubiquitin-proteasomal degradation of KCC2 during anesthesia is driven by E3 ligase Fbxl4. However, the mechanism by which ubiquitinated KCC2 is targeted to the proteasome has not been elucidated. We report in cultured neuro-2a cells that the valosin-containing protein (VCP) transported ubiquitinated KCC2 to the proteasome and in mice in vivo experiments that inhibition of VCP restored KCC2 expression in the VPM and enhanced the effects of anesthesia. In cultured neuro-2a cells, propofol-induced degradation of KCC2 was inhibited by VCP inhibitor DBeQ and VCP knockout plasmid sgRNA(VCP). Propofol-induced enhanced interaction between VCP and KCC2 was inhibited by knockout of Fbxl4 or Fas-associated factor 1 (FAF1). In in vivo studies, pharmacological or genetic inhibition of VCP in the VPM significantly prevented KCC2 degradation and enhanced propofol anesthesia; these effects were abrogated by a KCC2 antagonist VU0463271. These results demonstrate that the VCP controls ubiquitin-proteasomal degradation of KCC2 dependent on FAF1 recruitment and serves as a mechanism for the ubiquitin-proteasomal degradation of KCC2, which is responsible for the subsequent emergence from anesthesia.

Analyzing temporal imaging patterns in acute ischemic stroke via DICOM-timestamps

AbstractAcute stroke management is time-sensitive, making time data crucial for both research and quality management. However, these time data are often not reliably captured in routine clinical practice. In this proof-of-concept study we analysed image-based time data automatically captured in the DICOM format. We enrolled data from two separate stroke centers (n = 3136 and n = 2089). Data from the first center was additionally separated into groups with large-vessel-occlusion (LVO, n = 1.092), medium-vessel-occlusions (MVO, n = 416), and no occlusion (NVO, n = 1630). The DICOM-tag StudyTime was used to analyze the distribution of scan times throughout the day. Additionally, manually documented onset- and admission were extracted from the patients’ records in a subset of cases (n = 347). Timestamps were compared across centers and occlusion groups, and a probabilistic model was developed to illustrate and compare stroke occurrence patterns throughout the day. The temporal distribution of the scan times at both centers was exceptionally consistent with a peak around noon and a nighttime low. The groups with vessel occlusions showed an earlier peak compared to those without (p &lt; 0.04). The median interval between admission and scan time was 23 min, while the median onset-to-imaging time was 1 h:54 min. This proof-of-concept study indicates that DICOM-timestamps can reveal insights into the temporal patterns of stroke imaging and may be a promising tool for quality control and stroke research in general since they are always automatically captured by imaging devices as opposed to manual data collection in routine clinical practice.

Parallel vector memories or single memory updating?

Femtosecond laser versus manual clear corneal incision in implantable collamer lens surgery

Structural basis of nearest-neighbor cooperativity in the ring-shaped gene regulatory protein TRAP from protein engineering and cryo-EM

The homo-dodecameric ring-shaped trp RNA binding attenuation protein (TRAP) from Alkalihalobacillus halodurans (Aha) binds up to twelve tryptophan ligands (Trp) and becomes activated to bind a specific sequence in the 5’ leader region of the trp operon mRNA, thereby downregulating biosynthesis of Trp. Thermodynamic measurements of Trp binding have revealed a range of cooperative behavior for different TRAP variants, even if the averaged apparent affinities for Trp have been found to be similar. Proximity between the ligand binding sites, and the ligand-coupled disorder-to-order transition has implicated nearest-neighbor interactions in cooperativity. To establish a solid basis for describing nearest-neighbor cooperativity in TRAP, we engineered variants constructed with two subunits connected by a flexible linker (dTRAP). We mutated the binding sites of alternating protomers such that only every other site was competent for Trp binding (WT-Mut dTRAP). Ligand binding monitored by NMR, calorimetry, and native mass spectrometry revealed strong cooperativity in dTRAP containing adjacent binding-competent sites, but a severe binding defect when the wild-type sites were separated by mutated sites. Cryo-EM experiments of dTRAP in its ligand-free apo state, and both dTRAP and WT-Mut dTRAP in the presence of Trp, revealed progressive stabilization of loops that gate the Trp binding site and participate in RNA binding. These studies provide important insights into the thermodynamic and structural basis for the observed ligand binding cooperativity in TRAP. Such insights can be useful for understanding allosteric control networks and for the development of those with defined ligand sensitivity and regulatory control.

Inosine monophosphate dehydrogenase 2 (IMPDH2) modulates response to therapy and chemo-resistance in triple negative breast cancer

AbstractTriple negative breast cancer (TNBC) is one of the deadliest subtypes of breast cancer, whose high frequency of relapse is often due to resistance to chemotherapy. Here, we identify inosine monophosphate dehydrogenase 2 (IMPDH2) as a contributor to doxorubicin resistance, in multiple TNBC models. Analysis of publicly available datasets reveals elevated IMPDH2 expression to associate with worse overall TNBC prognosis in the clinic, including lower recurrence-free survival post adjuvant/neoadjuvant therapy. Importantly, both genetic depletion and pharmacological inhibition of IMPDH2 leads to reduction of pro-tumorigenic phenotypes in multiple doxorubicin-resistant TNBC models, both in vitro and in vivo. Overall, we propose IMPDH2 as a novel vulnerability that could be leveraged therapeutically to suppress and/or prevent the growth of chemo-resistant lesions.

Collaborative management partnerships strongly decreased deforestation in the most at-risk protected areas in Africa since 2000

Collaborative management partnerships (CMPs) between state wildlife authorities and nonprofit conservation organizations to manage protected areas (PAs) have been used increasingly across Sub-Saharan Africa since the 2000s. They aim to attract funding, build capacity, and increase the environmental effectiveness of PAs. Our study documents the rise of CMPs, examines their current extent, and measures their effectiveness in protecting habitats. We combine statistical matching and Before-After-Control-Intervention regressions to quantify the impact of CMPs, using tree cover loss as a proxy. We identify 127 CMPs located in 16 countries. CMPs are more often located in remote PAs, with habitats that are least threatened by human activity. Our results indicate that, on average, each year in a CMP results in an annual decrease in tree cover loss of about 55% compared to PAs without CMPs. Where initial anthropogenic pressure was low, we measure no effect. Where it was high, we see a 66% decrease in tree cover loss. This highly heterogeneous effect illustrates the importance of moving beyond average effect size when assessing conservation interventions, as well as the need for policy makers to invest public funds to protect the areas the most at risk.

Intestinal tissue levels of anti-TNF alpha, antibodies, and cytokines in paediatric Crohn disease

Complex tissue regeneration in <i>Lophuromys</i> reveals a phylogenetic signal for enhanced regenerative ability in deomyine rodents

Identifying why complex tissue regeneration is present or absent in specific vertebrate lineages has remained elusive. One also wonders whether the isolated examples where regeneration is observed represent cases of convergent evolution or are instead the product of phylogenetic inertia from a common ancestral program. Testing alternative hypotheses to identify genetic regulation, cell states, and tissue physiology that explain how regenerative healing emerges in some species requires sampling multiple species among which there is variation in regenerative ability across a phylogenetic framework. Here, we interrogate tissue healing across eleven rodents and show that brush-furred mice ( Lophuromys zena ) are capable of musculoskeletal regeneration where new tissue faithfully maintains axial polarity and tissue identity as previously observed in spiny mice ( Acomys spp. ). In contrast, we find that all nondeomyine rodents heal identical ear pinna injuries via fibrotic repair with scar tissue. Together, these data reveal a phylogenetic signal for enhanced regenerative ability in Deomyinae which is key to testing evolutionary hypotheses about the emergence of regenerative ability in mammals.