bluuebunny/crossref_metadata_2025 huggingface dataset:
The effects of dietary net energy on grow-finish performance and carcass characteristics of market gilts managed with immunological suppression of ovarian function and estrus (Improvest)
Authors: Bohrer Benjamin M , Wang Yifei , Landero Jose L , Young Malachy , Hansen Blaine , Pollmann D Steve , Mellencamp Marnie A , Van De Weyer Leanne , Aldaz Alvaro
Published: March 2024

The objective was to determine the effects of net energy (NE) during the grow-finish period on live performance and carcass characteristics of market gilts managed with immunological suppression of ovarian function and estrus (Improvest®; IMP) compared with market gilts not managed with Improvest (CON). The 104-d study began when 1,008 gilts (11 wk old; average starting weight of 30.8 kg) were allocated by weight to 48 pens with 21 gilts/pen. Half of the pens were randomly selected to be managed with Improvest while the other half of the pens were not managed with Improvest. Three dietary programs differing in their NE were formulated over five dietary phases (according to standardized ileal digestible lysine requirements) to provide an average of 2,218 kcal/kg (low NE), 2,343 kcal/kg (medium NE), or 2,468 kcal/kg (high NE). The experiment was designed as a 2 × 3 factorial with main effects of Improvest management and NE. For the overall study period, there were no significant interactions (P ≥ 0.20) for average daily feed intake (ADFI), average daily gain (ADG), or Gain:Feed (G:F). There were also no significant interactions between Improvest management and NE (P ≥ 0.30) for carcass characteristics. However, IMP gilts consumed more feed (6.8% greater ADFI; P < 0.01), grew faster (5.0% greater ADG; P < 0.01), were less efficient (1.8% lower G:F; P < 0.01), heavier (3.5 kg hot carcass weight; P < 0.01), and fatter (1.9 mm greater backfat thickness and 1.26% less predicted lean carcass yield; P < 0.01). No difference (P = 0.21) in carcass dressing percentage between IMP and CON gilts was reported. For the overall study period, gilts fed low NE and medium NE diets consumed more feed compared with gilts fed high NE diets (6.8% more ADFI for low NE and 5.7% more for medium NE; P < 0.01), and gilts fed low NE diets grew 2.5% slower (P < 0.01) than gilts fed medium NE diets, while gilts fed high NE diets were intermediate and not different from the other NE treatments. This resulted in gilts fed Low NE diets being the least efficient (3.8% lower G:F than medium NE and 7.1% lower G:F than High NE; P < 0.01). Overall, these data indicate that typical Improvest response levels were sustained at each of the NE treatments evaluated in this study as there were no significant interactions for Improvest management and NE; however, consideration should still be provided to the known production impacts of low NE diets.
Revision of the genus Robbea (Stilbonematinae: Desmodoridae), worldwide abundant marine nematodes with chromophoric Fe–Br inclusions and the description of a new stilbonematine genus
Authors: Scharhauser Florian , Saavedra Daniel E M , Pröts Philipp , Ott Jörg A , Geier Benedikt , Gruber-Vodicka Harald R , Polikarpov Maxim , Bourenkov Gleb , Leisch Nikolaus
Published: March 2024

Nematodes are one of the most widespread and abundant animal taxa across aquatic and terrestrial environments. In marine shallow-water, porous sediments, members of the subfamily Stilbonematinae may be found in high numbers. Stilbonematinae are characterized by their coat of symbiotic bacteria, which give the nematodes a white appearance, while the nematodes themselves are usually colourless. We identified several species of the genus Robbea (Desmodoridae: Stilbonematinae) in which live specimens had a conspicuous dark purple coloration of the glandular sense organs (GSOs), highly specialized epidermal glands that are prominent in the Stilbonematinae. The dark inclusions in the GSOs of Robbea contained high concentrations of iron and bromide, regardless of their habitat. Morphological and phylogenetic analyses show that the genus Robbea is paraphyletic and we define the new genus Cyathorobbea gen. nov. for species with sucker-shaped post-pharyngeal supplements in males. Furthermore, we describe five new Robbea species from around the world. Some Robbea species are morphologically very similar and required the use of principal component analysis of morphometric data to untangle the diversity in this taxon. Our work emphasizes the value of live animal observations that enable the identification of important characters and highlights the overlooked diversity within the Stilbonematinae.
TOMMicroNet: Convolutional Neural Networks for Smartphone-Based Microscopic Detection of Tomato Biotic and Abiotic Plant Health Issues
Authors: Sentil Sruthi , Choudhary Manoj , Tirsaiwala Mubin , RVS Sandeep , Suresh Vignesh Mahalingam , Jacob Chacko , Paret Mathews
Published: March 2024

The image-based detection and classification of plant diseases has become increasingly important to the development of precision agriculture. We consider the case of tomato, a high-value crop supporting the livelihoods of many farmers around the world. Many biotic and abiotic plant health issues impede the efficient production of this crop, and laboratory-based diagnostics are inaccessible in many remote regions. Early detection of these plant health issues is essential for efficient and accurate response, prompting exploration of alternatives for field detection. Considering the availability of low-cost smartphones, artificial intelligence-based classification facilitated by mobile phone imagery can be a practical option. This study introduces a smartphone-attachable 30× microscopic lens, used to produce the novel tomato microimaging data set of 8,500 images representing 34 tomato plant conditions on the upper and lower sides of leaves as well as on the surface of tomato fruits. We introduce TOMMicroNet, a 14-layer convolutional neural network (CNN) trained to classify biotic and abiotic plant health issues, and we compare it against six existing pretrained CNN models. We compared two separate pipelines of grouping data for training TOMMicroNet, either presenting all data at once or separating the data into subsets based on the three parts of the plant. Comparing configurations based on cross-validation and F1 scores, we determined that TOMMicroNet attained the highest performance when trained on the complete data set, with 95% classification accuracy on both training and external data sets. Given TOMMicroNet's capabilities when presented with unfamiliar data, this approach has potential for the identification of plant health issues.
A Review of Current Uses of Amniotic Membrane Transplantation in Ophthalmic Plastic and Reconstructive Surgery
Authors: Parikh Alomi O. , Conger Jordan R. , Li Joy , Sibug Saber Maria , Chang Jessica R.
Published: March 2024

Purpose:

To review and summarize the existing literature on the clinical applications of amniotic membrane transplantation (AMT) in ophthalmic plastic and reconstructive surgery.

Methods:

A literature review was conducted on the PubMed database using the following search terms: “amniotic membrane” and “eyelid” or “orbit” or “fornix” or “socket” or “lacrimal”.

Results:

In total 516 articles resulted from the search, of which 62 were included. Numerous cases and case series have been published on the use of amniotic membrane transplantation for ocular surface reconstruction, eyelid and forniceal reconstruction, and cicatricial eyelid abnormalities. Surgical methods of securing the graft vary. Few comparative studies exist; some show a similar or improved result when compared to oral mucous membrane grafting for certain indications.

Conclusions:

Amniotic membrane transplantation can be a useful tool for the oculoplastic surgeon when faced with a case requiring reconstruction of the posterior lamellae, particularly in patients without other graft donor sites available, and uses of AMT continue to expand. Additional studies directly comparing AMT to other reconstructive techniques would be helpful in choosing between the available surgical techniques and standardizing best practices.
IgG4-related Orbital Disease Presenting as an Orbital Apex Lesion
Authors: Ang Terence , Tong Jessica Y. , Davis Garry , Selva Dinesh
Published: March 2024

IgG4-related disease is an uncommon multisystem inflammatory disease characterized by tissue infiltration by IgG4 plasma cells, extensive fibrosis, and sclerosing inflammation. Diffuse orbital involvement extending to the orbital apex and cavernous sinus has been reported, but a solitary well-circumscribed lesion at the apex has not been previously reported. Herein, we report a unique case of IgG4-related orbital disease presenting as a solitary well-circumscribed orbital apex lesion causing subacute visual decline in a 45-year-old male. MRI demonstrated bilateral lacrimal gland and infraorbital nerve enlargement and an 18 × 7 mm left orbital apex lesion demonstrating homogeneous contrast enhancement and isointense signal on T2. He was initially treated with tapering systemic corticosteroid therapy with improvement in his vision; however, he experienced visual deterioration 3 months later with recurrent inflammation. He subsequently commenced high-dose systemic corticosteroid therapy and rituximab infusions with improvement of left visual acuity to 6/7.5 + 2.
Plasma Exeresis for the Treatment of Benign Eyelid Lesions: A New Surgical Approach
Authors: Ucar Fikret , Unluzeybek Murat
Published: March 2024

Purpose:

To report the plasma therapy technique and its clinical outcomes in patients with benign eyelid lesions.

Methods:

This is a retrospective, noncomparative, interventional study. The study included 71 eyes of 66 patients who underwent plasma exeresis for benign eyelid lesions in our clinic between February 2018 and December 2022. Patient symptoms, cosmetic outcomes, and complications were evaluated.

Results:

The lesions were removed with a single plasma exeresis treatment in all patients. The mean size of the lesion at its largest part was 5.5 ± 1.2 mm (range, 3.0–8.8 mm). No complications were encountered during the procedure. The mean procedure time was 4.0 ± 0.7 minutes (range, 3–6 minutes). Postoperatively, only 3 cases (4.2%) with tarsal conjunctival extension had mild irritation symptoms such as pain, discomfort, and redness. The treated areas were fully improved cosmetically, and all patients were satisfied with the cosmetic outcomes.

Conclusions:

The plasma therapy technique for removing benign eyelid lesions offers minimally invasive surgery, less discomfort, fast recovery, and successful anatomical and cosmetic outcomes.
Definitions, outcomes and perspectives for oligometastatic bladder cancer: towards a standardized terminology
Authors: Calleris Giorgio , von Deimling Markus , Kesch Claudia , Soria Francesco , Gontero Paolo , Ploussard Guillaume , Laukhtina Ekaterina , Pradere Benjamin
Published: March 2024

Purpose of review

Oligometastatic (om) cancer is considered as a transitional state in between locally confined disease and widespread metastases, accessible to a multimodal treatment, combining systemic and local therapy. In urothelial bladder cancer (BCa), the definitions and the approaches to this condition are poorly standardised and mainly based on retrospective data. We aim to portray the framework for uro-oncologic terminology in omBCa and go through the latest evidence and the future perspectives.

Recent findings

Retrospective and registry data support the potential benefits of multimodality treatment for carefully selected omBCa patients, especially following a good response to systemic treatment. In 2023, a Delphi consensus has defined omBCa, allowing maximum three metastatic lesions, theoretically amenable to radical local treatment. In de-novo omBCa, surgical treatment of primary tumour might improve overall survival (OS), according to a matched registry analysis; also, consolidative radiotherapy was associated with better OS in two recent cohorts. Furthermore, metastasis-directed therapy (MDT) has shown high local control rates and promising OS (14.9–51 months) in a meta-analysis; benefits might be more pronounced for single-site omBCa and nodal or lung lesions.

From a clinical perspective, in de-novo omBCa, the local treatment of primary and metastatic sites might improve disease control and survival, in selected patients; in the oligorecurrent setting, MDT achieves good local symptom control with limited side effects; in selected cases, it could convey a survival benefit, too. From a research perspective, well designed prospective evidence is eagerly awaited, based on recently adopted shared definitions for omBCa.
Can 18F-FES PET Improve the Evaluation of 18F-FDG PET in Patients With Metastatic Invasive Lobular Carcinoma?
Authors: Liu Cheng , Ma Guang , Xu Xiaoping , Song Shaoli , Yang Zhongyi
Published: March 2024

Purpose

Invasive lobular carcinoma (ILC) exhibits a low affinity for 18F-FDG. The estrogen receptor (ER) is commonly expressed in ILCs, suggesting a potential benefit of targeting with the ER probe 18F-FES in this patient population. The objective of this study was to evaluate the diagnostic performance of 18F-FES imaging in patients with metastatic ILC and compare it with that of 18F-FDG.

Methods

We conducted a retrospective analysis of 20 ILC patients who underwent concurrent 18F-FES and 18F-FDG PET/CT examinations in our center. 18F-FES and 18F-FDG imaging were analyzed to determine the total count of tracer-avid lesions in nonbone sites and their corresponding organ systems, assess the extent of anatomical regions involved in bone metastases, and measure the SUVmax values for both tracers.

Results

Among 20 ILC patients, 65 nonbone lesions were found to be distributed in 13 patients, and 16 patients were diagnosed with bone metastasis, which was distributed in 54 skeletal anatomical regions. The detection rate of 18F-FDG in nonbone lesions was higher than that of 18F-FES (57 vs 37, P < 0.001). 18F-FES demonstrated a superior ability to detect nonbone lesions in 4 patients, whereas 18F-FDG was superior in 5 patients (P > 0.05). Among 9/16 patients with bone metastasis, 18F-FES demonstrated a significant advantage in the detection of bone lesions compared with 18F-FDG (P = 0.05). Furthermore, patients with only 18F-FES–positive lesions (12/12) were administered endocrine regimens, whereas patients lacking 18F-FES uptake (2/3) predominantly received chemotherapy.

Conclusions

18F-FES is more effective than 18F-FDG in detecting bone metastasis in ILC, but it does not demonstrate a significant advantage in nonbone lesions. Additionally, the results of examination with 18F-FES have the potential to guide patient treatment plans.
FDG PET/CT Findings of a Small Cell Carcinoma of the Lung Presented as Diffuse Dermatomyositis
Authors: Li Xinyu , Tian Bin , Bai Xia
Published: March 2024

Patients with dermatomyositis are prone to have occult malignancy. A previously healthy 68-year-old man with dermatomyositis underwent FDG PET/CT to detect possible malignancy of unknown origin. The images showed not only diffuse increased activity in the muscle, which was related to the known dermatomyositis, but also intense activity in the anterior chest with foci of abnormal activity throughout the body. Pathology examination confirmed small cell carcinoma of the lung with widespread metastases.
Macrophages foster adaptive anti-tumor immunity by ZEB1-dependent cytotoxic T cell chemoattraction
Authors: Fuchs Kathrin , Armstark Isabell , van Roey Ruthger , Hajjaj Yussuf , D’Avanzo Elisabetta , Liguori Renato , Ferrazzi Fulvia , Ackermann Jochen , Amon Lukas , Alfredo Marwin , Faas Maria , Hübner Julian , Hoffmann Markus H , Krönke Gerhard , Becker Christoph , Dudziak Diana , Nimmerjahn Falk , Brabletz Simone , Stemmler Marc P. , Brabletz Thomas , Schuhwerk Harald
Published: March 2024

Tumor-associated macrophages (TAMs) shape the tumor microenvironment (TME) and exert a decisive impact on anti-tumor immunity. Understanding TAM function is therefore critical to understand anti-tumor immune responses and to design immunotherapies. Here, we describe the transcription factor ZEB1, a well-known driver of epithelial-to-mesenchymal transition, as an intrinsic regulator of TAM function in adaptive anti-tumor immunity. By combining cell type-specific deletion of Zeb1 with syngeneic models of colorectal and pancreatic cancer, we discovered an unexpected function of ZEB1 in the TAM-mediated control of T cell trafficking. ZEB1 supports secretion of a subset of chemokines including CCL2 and CCL22 by promoting their transcription and translation as well as by safeguarding protein processing. ZEB1 thereby elevates cytotoxic T cell (CTL) recruitmentin vitroandin vivoand fosters immunosurveillance during tumor as well as lung metastatic outgrowth. Our study spotlights ZEB1 as a crucial facilitator of adaptive anti-tumor immunity and uncovers a potential therapeutic window of opportunity for cytokine-guided enhancement of CTL infiltration into tumors and metastases.
High-Resolution Spatial Transcriptomic Atlas of Mouse Soleus Muscle: Unveiling Single Cell and Subcellular Heterogeneity in Health and Denervation
Authors: Hsu Jer-En , Ruiz Lloyd , Hwang Yongha , Guzman Steve , Cho Chun-Seok , Cheng Weiqiu , Si Yichen , Macpherson Peter , Schrank Mitchell , Jun Goo , Kang Hyun-Min , Kim Myungjin , Brooks Susan , Lee Jun Hee
Published: March 2024

Skeletal muscle is essential for both movement and metabolic processes, characterized by a complex and ordered structure. Despite its importance, a detailed spatial map of gene expression within muscle tissue has been challenging to achieve due to the limitations of existing technologies, which struggle to provide high-resolution views. In this study, we leverage the Seq-Scope technique, an innovative method that allows for the observation of the entire transcriptome at an unprecedented submicron spatial resolution. By applying this technique to the mouse soleus muscle, we analyze and compare the gene expression profiles in both healthy conditions and following denervation, a process that mimics aspects of muscle aging. Our approach reveals detailed characteristics of muscle fibers, other cell types present within the muscle, and specific subcellular structures such as the postsynaptic nuclei at neuromuscular junctions, hybrid muscle fibers, and areas of localized expression of genes responsive to muscle injury, along with their histological context. The findings of this research significantly enhance our understanding of the diversity within the muscle cell transcriptome and its variation in response to denervation, a key factor in the decline of muscle function with age. This breakthrough in spatial transcriptomics not only deepens our knowledge of muscle biology but also sets the stage for the development of new therapeutic strategies aimed at mitigating the effects of aging on muscle health, thereby offering a more comprehensive insight into the mechanisms of muscle maintenance and degeneration in the context of aging and disease.
CAR-engineered lymphocyte persistence is governed by a FAS ligand/FAS auto-regulatory circuit
Authors: Yi Fei , Cohen Tal , Zimmerman Natalie , Dündar Friederike , Zumbo Paul , Eltilib Razan , Brophy Erica J. , Arkin Hannah , Feucht Judith , Gormally Michael V. , Hackett Christopher S. , Kropp Korbinian N. , Etxeberria Inaki , Chandran Smita S. , Park Jae H. , Hsu Katharine C. , Sadelain Michel , Betel Doron , Klebanoff Christopher A.
Published: March 2024

Chimeric antigen receptor (CAR)-engineered T and NK cells can cause durable remission of B-cell malignancies; however, limited persistence restrains the full potential of these therapies in many patients. The FAS ligand (FAS-L)/FAS pathway governs naturally-occurring lymphocyte homeostasis, yet knowledge of which cells express FAS-L in patients and whether these sources compromise CAR persistence remains incomplete. Here, we constructed a single-cell atlas of diverse cancer types to identify cellular subsets expressingFASLG, the gene encoding FAS-L. We discovered thatFASLGis limited primarily to endogenous T cells, NK cells, and CAR-T cells while tumor and stromal cells express minimalFASLG. To establish whether CAR-T/NK cell survival is regulated through FAS-L, we performed competitive fitness assays using lymphocytes modified with or without a FAS dominant negative receptor (ΔFAS). Following adoptive transfer, ΔFAS-expressing CAR-T and CAR-NK cells became enriched across multiple tissues, a phenomenon that mechanistically was reverted throughFASLGknockout. By contrast,FASLGwas dispensable for CAR-mediated tumor killing. In multiple models, ΔFAS co-expression by CAR-T and CAR-NK enhanced antitumor efficacy compared with CAR cells alone. Together, these findings reveal that CAR-engineered lymphocyte persistence is governed by a FAS-L/FAS auto-regulatory circuit.
Deciphering Mechanochemical Influences of Emergent Actomyosin Crosstalk using QCM-D
Authors: Kerivan Emily M. , Amari Victoria N. , Weeks William B. , Hardin Leigh H. , Tobin Lyle , Azzam Omayma Y. Al , Reinemann Dana N.
Published: March 2024

Purpose

Cytoskeletal protein ensembles exhibit emergent mechanics where behavior exhibited in teams is not necessarily the sum of the components’ single molecule properties. In addition, filaments may act as force sensors that distribute feedback and influence motor protein behavior. To understand the design principles of such emergent mechanics, we developed an approach utilizing QCM-D to measure how actomyosin bundles respond mechanically to environmental variables that alter constituent myosin II motor behavior.

Methods

QCM-D is used for the first time to probe alterations in actin-myosin bundle viscoelasticity due to changes in skeletal myosin II concentration and motor nucleotide state. Actomyosin bundles were constructed on a gold QCM-D sensor using a microfluidic setup, and frequency and dissipation change measurements were recorded for each component addition to decipher which assay constituents lead to changes in bundle structural compliancy.

Results

Lowering myosin concentration is detected as lower shifts in frequency and dissipation, while the relative changes in frequency and dissipation shifts for both the first and second actin additions are relatively similar. Strikingly, buffer washes with different nucleotides (ATP vs. ADP) yielded unique signatures in frequency and dissipation shifts. As myosin II’s ADP-bound state tightly binds actin filaments, we observe an increase in frequency and decrease in dissipation change, indicating a decrease in viscoelasticity, likely due to myosin’s increased affinity for actin, conversion from an active motor to a static crosslinker, and ability to recruit additional actin filaments from the surface, making an overall more rigid sensor coating. However, lowering the ADP concentration results in increased system compliancy, indicating that transient crosslinking and retaining a balance of motor activity perhaps results in a more cooperative and productive force generating system.

Conclusions

QCM-D can detect changes in actomyosin viscoelasticity due to molecular-level alterations, such as motor concentration and nucleotide state. These results provide support for actin’s role as a mechanical force-feedback sensor and demonstrate a new approach for deciphering the feedback mechanisms that drive emergent cytoskeletal ensemble crosstalk and intracellular mechanosensing. This approach can be adapted to investigate environmental influences on more complex cytoskeletal ensemble mechanics, including addition of other motors, crosslinkers, and filament types.
Modular, Vascularized Hypertrophic Cartilage Constructs for Bone Tissue Engineering Applications
Authors: Schott Nicholas G. , Kaur Gurcharan , Coleman Rhima , Stegemann Jan P.
Published: March 2024

Insufficient vascularization is a main barrier to creating engineered bone grafts for treating large and ischemic defects. Modular tissue engineering approaches have promise in this application because of the ability to combine tissue types and to localize microenvironmental cues to drive desired cell function. In direct bone formation approaches, it is challenging to maintain sustained osteogenic activity, since vasculogenic cues can inhibit tissue mineralization. This study harnessed the physiological process of endochondral ossification to create multiphase tissues that allowed concomitant mineralization and vessel formation. Mesenchymal stromal cells in pellet culture were differentiated toward a cartilage phenotype, followed by induction to chondrocyte hypertrophy. Hypertrophic pellets exhibited increased alkaline phosphatase activity, calcium deposition, and osteogenic gene expression relative to chondrogenic pellets. In addition, hypertrophic pellets secreted and sequestered angiogenic factors, and supported new blood vessel formation by co-cultured endothelial cells and undifferentiated stromal cells. Multiphase constructs created by combining hypertrophic pellets and vascularizing microtissues and maintained in unsupplemented basal culture medium were shown to support robust vascularization and sustained tissue mineralization. These results demonstrate a newin vitrostrategy to produce multiphase engineered constructs that concomitantly support the generation of mineralize and vascularized tissue in the absence of exogenous osteogenic or vasculogenic medium supplements.

Graphical Abstract
Treponema pallidumperiplasmic and membrane proteins are recognized by circulating and skin CD4+ T cells
Authors: Reid Tara B. , Godornes Charmie , Campbell Victoria L. , Laing Kerry J. , Tantalo Lauren C. , Gomez Alloysius , Pholsena Thepthara N. , Lieberman Nicole A. P. , Krause Taylor M. , Cegielski Victoria I. , Culver Lauren A. , Nguyen Nhi , Tong Denise Q. , Hawley Kelly L. , Greninger Alexander L. , Giacani Lorenzo , Cameron Caroline E. , Dombrowski Julia C. , Wald Anna , Koelle David M.
Published: March 2024

Background

Histologic and serologic studies suggest the induction of local and systemicTreponema pallidum(Tp)-specific CD4+ T cell responses toTpinfection. We hypothesized thatTp-specific CD4+ T cells are detectable in blood and in the skin rash of secondary syphilis and persist in both compartments after treatment.

Methods

PBMC collected from 67 participants were screened by IFNγ ELISPOT response toTpsonicate.Tp-reactive T cell lines from blood and skin were probed for responses to 88 recombinantTpantigens. Peptide epitopes and HLA class II restriction were defined for selected antigens.

Results

We detected CD4+ T cell responses toTpsonicate ex vivo. UsingTp-reactive T cell lines we observed recognition of 14 discrete proteins, 13 of which localize to bacterial membranes or the periplasmic space. After therapy,Tp-specific T cells persisted for at least 6 months in skin and 10 years in blood.

Conclusions

Tpinfection elicits an antigen-specific CD4+ T cell response in blood and skin.Tp-specific CD4+ T cells persist as memory in both compartments long after curative therapy. TheTpantigenic targets we identified may be high priority vaccine candidates.
Chemical tools to expand the ligandable proteome: diversity-oriented synthesis-based photoreactive stereoprobes
Authors: Ogasawara Daisuke , Konrad David B. , Tan Zher Yin , Carey Kimberly L. , Luo Jessica , Won Sang Joon , Li Haoxin , Carter Trever , DeMeester Kristen E. , Njomen Evert , Schreiber Stuart L. , Xavier Ramnik J. , Melillo Bruno , Cravatt Benjamin F.
Published: March 2024

Chemical proteomics enables the global assessment of small molecule-protein interactions in native biological systems and has emerged as a versatile approach for ligand discovery. The range of small molecules explored by chemical proteomics has, however, been limited. Here, we describe a diversity-oriented synthesis (DOS)-inspired library of stereochemically-defined compounds bearing diazirine and alkyne units for UV light-induced covalent modification and click chemistry enrichment of interacting proteins, respectively. We find that these ‘photo-stereoprobes’ interact in a stereoselective manner with hundreds of proteins from various structural and functional classes in human cells and demonstrate that these interactions can form the basis for high-throughput screening-compatible nanoBRET assays. Integrated phenotypic analysis and chemical proteomics identified photo-stereoprobes that modulate autophagy by engaging the mitochondrial serine protease CLPP. Our findings show the utility of photo-stereoprobes for expanding the ligandable proteome, furnishing target engagement assays, and discovering and characterizing bioactive small molecules by cell-based screening.
Non-Electrostatic Basis for an Artificial Metalloenzyme Catalysis
Authors: Mukherjee Anagh , Roy Subhendu
Published: March 2024

The artificial metalloenzyme (referred to asIr-Q) reported by Hartwig and coworkers presented an important milestone in merging the extraordinary efficiency of biocatalyst with the versatility of small molecule chemical catalyst in catalyzing a new-to-nature carbene insertion reaction. The artificial enzyme results from formal replacement of the Fe by an Ir(Me) moiety along with four C317G, T213G, L69V, V254L mutations in a natural Cytochrome enzyme CYP119 by directed evolution method. Importantly, this is a show-stopper enzyme as it exhibits a catalytic rate enhancement similar to that of natural enzymes. Despite this remarkable discovery, there is no mechanistic understanding as to why it displays extraordinary efficiency, so far been intractable to experimental methods. In this study, we have deciphered the ‘catalytically active conformation’ ofIr-Qusing large-scale molecular dynamics simulations and rigorous quantum chemical calculations. Our study reveals how directed evolution mutations precisely position the cofactor-substrate in an unusual orientation within a reshaped active site that emerged during evolution and fostered by C−H…π interactions from more ordered mutated L69V and V254L residues. This productive conformation correctly reproduces the experimental barrier height and the catalytic effect of 2.7 kcal/mol, in excellent agreement with observed rate enhancement. Moreover, the active conformation features an unprecedented bonding interaction in a metal-carbene species that preferentially stabilizes the rate determining formation of an Iridium-Porphyrin Carbene intermediate to render the observed high catalytic rate acceleration. While the electrostatic criteria are widely established, this study suggests a new design paradigm towards realization of fully programmable protein catalysis.
How to quantify developmental synchrony in malaria parasites
Authors: Greischar Megan A. , Savill Nicholas J. , Reece Sarah E. , Mideo Nicole
Published: March 2024

Malaria infections represent an iconic example of developmental synchrony, where periodic fevers can result when the population of parasites develops synchronously within host red blood cells. The level of synchrony appears to vary across individual hosts and across parasite species and strains, variation that—once quantified—can illuminate the ecological and evolutionary drivers of synchrony. Yet current approaches for quantifying synchrony in parasites are either biased by population dynamics or unsuitable when population growth rates vary through time, features ubiquitous to parasite populationsin vitroandin vivo. Here we develop an approach to estimate synchrony that accounts for population dynamics, including changing population growth rates, and validate it with simulated time series data encompassing a range of synchrony levels in two different host-parasite systems: malaria infections of mice and human malaria parasitesin vitro. This new method accurately quantifies developmental synchrony from per capita growth rates using obtainable abundance data even with realistic sampling noise, without the need to sort parasites into developmental stages. Our approach enables variability in developmental schedules to be disentangled from even extreme variation in population dynamics, providing a comparative metric of developmental synchrony.
Increased dosage of wild-type KRAS protein drivesKRAS-mutant lung tumorigenesis and drug resistance
Authors: Ivanisevic Tonci , Magits Wout , Ma Yan , Zhao Peihua , Van Boxel Emiel , Lechat Benoit , Stites Edward , Vande Velde Greetje , Sewduth Raj , Sablina Anna
Published: March 2024

Almost 30% of lung adenocarcinomas are driven by activatingKRASmutations. The heterogeneous clinical behavior observed in these cancers could be due to the imbalance of wild-type and oncogenic KRAS alleles. However, the role of RAS dysregulation at the protein level needs to be further explored. A genome-wide global protein stability screen identified the CUL3 ubiquitin ligase adaptor LZTR1, as a major proteostatic regulator of wild-type but not mutant KRAS. InKRAS-mutant lung adenocarcinoma, shallow deletion ofLZTR1is observed in up to 50% of patients and is associated with hypoxic signatures and poorer progression-free disease survival. In aKras-mutant lung cancer mouse model, heterozygous loss ofLztr1promoted tumor growth, led to peritumoral vascular remodeling, and limited the response to the KRAS-G12D inhibitor MRTX1133. The vascular alteration inLZTR1-depleted lung cancer was mediated by increased wild-type KRAS protein dosage, which promoted mTOR pathway activation and a subsequent increase in VEGFA secretion. The inhibition of the PI3K/mTOR pathway using dactolisib normalized tumor vasculature, improved drug delivery, and overcame resistance to KRAS-G12D inhibitors. In summary, the dysregulation of RAS proteostasis contributes to lung tumorigenesis, and targeting wild-type KRAS signaling is crucial to overcome intrinsic resistance to inhibitors of mutant KRAS.

Significance

Our study highlights the impact of RAS proteostasis on lung cancer development and progression. Vascular normalization achieved by suppressing wild-type KRAS signaling improved the delivery and response to MRTX1133 inKRAS-mutant lung cancer with shallowLZTR1deletion.
Investigating the mechanisms of antibody binding to alpha-synuclein for the treatment of Parkinson’s Disease
Authors: Harrison Malcolm C. , Lai Pin-Kuang
Published: March 2024

Parkinson’s Disease (PD) is an idiopathic neurodegenerative disorder with the second-highest prevalence rate behind Alzheimer’s Disease. The pathophysiological hallmarks of PD are both degeneration of dopaminergic neurons in the substantia nigra pars compacta and the inclusion of misfolded alpha-synuclein (α-syn) aggregates known as Lewy bodies. Despite decades of research for potential PD treatments, none have been developed, and developing new therapeutic agents is a time-consuming and expensive process. Computational methods can be used to investigate the properties of drug candidates currently undergoing clinical trials to determine their theoretical efficiency at targeting α-syn. Monoclonal antibodies (mAbs) are biological drugs with high specificity, and Prasinezumab (PRX002) is a mAb currently in Phase II, which targets the C-terminus (AA 118-126) of α-syn. We utilized BioLuminate and PyMol for structure prediction and preparation of the fragment antigen-binding (Fab) region of PRX002 and 34 different conformations of α-syn. Protein-protein docking simulations were performed using PIPER, and 3 of the docking poses were selected based on the best fit. Molecular dynamics simulations were conducted on the docked protein structures for 1000 ns, and hydrogen bonds, electrostatic, and hydrophobic interactions were analyzed using MDAnalysis to determine which residues were interacting and how often. Hydrogen bonds were shown to form frequently between the HCDR2 region of PRX002 and α-syn. Free energy was calculated to determine binding affinity. The predicted binding affinity shows a strong antibody-antigen attraction between PRX002 and α-syn. RMSD was calculated to determine the conformational change of these regions throughout the simulation. The mAb’s developability was determined using computational screening methods. Our results demonstrate the efficiency and developability of this therapeutic agent.
Mimicking anin celluloenvironment for enzyme-free paper-based nucleic acid tests at the point of care
Authors: Beard Jeffrey W. , Hunt Samuel L. , Evans Alexander , Goenner Coleman , Miller Benjamin L.
Published: March 2024

Point of care (PoC) nucleic acid amplification tests (NAATs) are a cornerstone of public health, providing the earliest and most accurate diagnostic method for many communicable diseases, such as HIV, in the same location the patient receives treatment. Communicable diseases disproportionately impact low-resource communities where NAATs are often unobtainable due to the resource intensive enzymes that drive the tests. Enzyme-free nucleic acid detection methods, such as hybridization chain reaction (HCR), use DNA secondary structures for self-driven amplification schemes producing large DNA nanostructures and capable of single molecule detectionin cellulo. These thermodynamically driven DNA-based tests have struggled to penetrate the PoC diagnostic field due to their inadequate limits of detection or complex workflows. Here we present a proof-of-concept NAAT that combines HCR-based amplification of a target nucleic acid sequence with paper-based nucleic acid filtration and enrichment capable of detecting sub pM levels of synthetic DNA. We reconstruct the favorable hybridization conditions of anin celluloreactionin vitroby incubating HCR in an evaporating, microvolume environment containing poly(ethylene glycol) as a crowding agent. We demonstrate that the kinetics and thermodynamics of DNA-DNA and DNA-RNA hybridization is enhanced by the dynamic evaporating environment and inclusion of crowding agents, bringing HCR closer to meeting PoC NAAT needs.
Identification of Myocardial Infarction (MI) Probability from Imbalanced Medical Survey Data: An Artificial Neural Network (ANN) with Explainable AI (XAI) Insights
Authors: Akter Simon Bin , Akter Sumya , Pias Tanmoy Sarkar , Eisenberg David , Fernandez Jorge Fresneda
Published: March 2024

In the healthcare industry, many artificial intelligence (AI) models have attempted to overcome bias from class imbalances while also maintaining high results. Firstly, when utilizing a large number of unbalanced samples, current AI models and related research have failed to balance specificity and sensitivity – a problem that can undermine the reliability of medical research. Secondly, no reliable method for obtaining detailed interpretability has been put forth when addressing large numbers of input features. The present research addresses these two critical research gaps with a proposed lightweight Artificial Neural Network (ANN) model. Using 43 input features from the 2021 Behavioral Risk Factor Surveillance System (BRFSS) dataset, the proposed model outperforms prior models in producing balanced outcomes from markedly unbalanced large survey data. The efficacy of this proposed ANN model is attributed to its simplified design, which reduces processing demands, and its resilience in identifying the probability of myocardial infarction (MI). This is demonstrated by its 80% specificity and 77% sensitivity, and is substantiated by a Receiver Operating Characteristic Area Under the Curve (AUC) of 0.87. The outcomes across the scopes of each specified data domain were also separately represented, thus demonstrating the proposed model’s robust sensitivity. The interpretability of the model, as measured by Shapley values, reveals substantial correlations between myocardial infarction (MI) and its risk factors, including long-term medical conditions, socio-demographic factors, personal health habits, economic and social status, healthcare availability and affordability, as well as impairment statuses, providing valuable insights for improved cardiovascular risk assessment and personalized healthcare strategies.
Alcohol consumption and long-term risk of gout in men and women: a prospective study addressing potential reverse causation
Authors: Lyu Jie-Qiong , Peng Xian-Zhen , Wang Jia-Min , Miao Meng-Yuan , Tao Hao-Wei , Zhao Miao , Zhu Jie , Yang Jing , Chen Jing-Si , Qin Li-Qiang , Chen Wei , Chen Guo-Chong
Published: March 2024

Background

While specific alcoholic beverages have been associated with gout, the influence of residual confounding and potential reverse-causation bias on these associations remains to be addressed.

Methods

The exploratory analysis included 218,740 men and 271,389 women free of gout at recruitment of the UK Biobank. Among these, 181,925 men and 223,700 women remained for the final analysis where potential reverse causation was addressed, i.e., by excluding participants who had or were likely to have reduced alcohol intake due to health issues at baseline, in addition to cases that were identified within the first 2 years of follow-up.

Results

In the final analysis, current drinkers had a higher risk of gout than never drinkers in men (HR = 1.78, 95% CI: 1.39-2.28) but not in women (HR = 0.84, 95% CI: 0.68-1.03). Among current drinkers, higher alcohol consumption was associated a substantially higher risk of gout in men and a moderately higher risk in women. The most evident sex difference in the consumption of specific alcoholic beverages was observed for beer/cider (mean: 4.16 vs. 0.44 pints/week in men and women, respectively). Consumption of champagne/white wine, beer/cider, and spirits each was associated with a higher risk of gout in both sexes, with beer/cider showing the strongest association (HRper 1 pint/d= 1.55, 95% CI: 1.49-1.61 in men; HRper 1 pint/d= 1.71, 95% CI: 1.14-2.57 in women). In the exploratory analysis, low to moderate consumption of specific alcoholic beverages were widely associated with a lower risk of gout, whereas all these inverse associations were eliminated in the final analysis. For example, red wine intake was associated with a lower risk of gout in women in the exploratory analysis (HRper 1 glass/d= 0.79, 95% CI: 0.69-0.90), but not after adjusting for other alcoholic beverages and addressing potential reverse causation (HRper 1 glass/d= 0.91, 95% CI: 0.77-1.06).

Conclusions

Consumption of total and several specific alcoholic beverages is associated with a higher risk of gout in both sexes. The sex-specific associations for total alcohol consumption may be attributable to differences in the type of alcohol consumed rather than biological differences between men and women.
Factors that influence the caste ratio in a bacterial division of labour
Authors: Domínguez Luis Alfredo Avitia , Yu Zhengzhou , Chopra Varun , Merks Roeland , van Dijk Bram , Rozen Daniel
Published: March 2024

Colonies of the bacteriaStreptomyces coelicolordivide labour between cells that specialize on growth and sporulation and cells that specialize on antibiotic production. This division of labour arises due to costly chromosome deletions in the antibiotic overproducers. However, little is known about when and where these mutations occur or whether their frequency – which we liken to the caste ratio in social insects – is phenotypically plastic. To elucidate changes in the proportions of specialized cells (measured as the mutation frequency), we sampledS. coelicolorcolonies grown under different conditions. Temporally, mutation frequency increased linearly with colony age and size. Spatially, mutations accumulated disproportionately in the colony center, despite greater growth and sporulation at the periphery. Exposing colonies to sub-inhibitory concentrations of some antibiotics, a competitive cue inStreptomyces, increased mutation frequencies. Finally, direct competition with otherStreptomycesthat naturally produce antibiotics increased mutation frequencies, while also increasing spore production. Our findings provide insights into the intrinsic and environmental factors driving division of labor inStreptomyces coloniesby showing that mutation frequencies are dynamic and responsive to the competitive environment. These results show that chromosome deletions are phenotypically plastic and suggest thatStreptomycescan flexibly adjust their caste ratio.
Transposable Elements and piRNAs interaction prediction with Predictive Bi-Clustering Trees
Authors: Freire Oliveira Hiago , dos Santos Renato A. C. , Cerri Ricardo
Published: March 2024

PIWI-interacting RNAs (piRNAs) are a class of noncoding RNAs whose actions range from regulating gene expression to silencing Transposable Elements, characterized for being from 21 to 35 nucleotides long, displaying a uracil bias at the 5’ end, and a 2’-O-methylation at the 3’ end. Transposable Elements (TEs) are genetic elements that move within host genomes. TE replication can promote harmful recombination events by generating breaks in DNA double strands, in addition to interfering with expression. Silencing of these elements by piRNAs occurs in the germ line in most animals and is essential for maintaining genome integrity. In this work, the problem of in silico interaction prediction between piRNAs and TEs was addressed by a decision tree-based algorithm, namely Predictive Bi-Clustering Trees (PBCT). In order to improve the algorithm’s performance, the piRNA-TE interaction matrix was reconstructed using a Beta-distribution-rescored Neighborhood Regularized Logistic Matrix Factorization (NRLMFβ) algorithm. PBCT was tested in 5-fold and 10-fold cross-validation configurations, both with the original interaction matrix (BICT) and the interaction matrix reconstructed by NRLMFβ (BICTR). Although not being able to predict positive interactions satisfactorily given the huge dataset imbalance, advantages could be observed when using matrix factorization. Comparatively, in the BICT method, PBCT presented higher values of AUROC and AUPRC. However, in the BICTR method, PBCT was able to correctly predict more positive interactions, which are, in fact, the primary interest of this study. Potential biological applications and ways to improve the algorithm’s performance were also discussed.

Author summary

piRNAs and transposable elements are biomolecules that interact in the germ lime in most animals, such that piRNAs silence these elements to keep genome integrity. However, detecting which piRNA interacts with which TE is a laborious task with low results, given that the rules that govern these interactions still need to be fully elicited. In this paper, we addressed the interaction prediction pair piRNA-TE using a multi-label decision-tree-like algorithm called PBCT applied toin vivoknown interactions. Given that it is a Positive-Unlabeled Learning problem, since we cannot be sure of a biological negative interaction, we reconstructed the interaction matrix employing an NRLMFβ algorithm. We compared the results given the original interaction matrix and the reconstructed matrix. The results with this algorithm and parameters could have been better, even though the reconstruction has proven fruitful. Further, we addressed our problem with other multi-label learning approaches and briefly compared them. We also discussed potential biological applications and ways to improve the algorithm’s performance.