bluuebunny/crossref_metadata_2025_split huggingface dataset:
Angiotensin‐(1–7) Promotes Resolution of the Inflammatory Process of Asthma
Authors: Campagnole‐Santos Maria Jose , Magalhaes Giselle Santos , Rodrigues‐Machado M Gloria , Gregorio Juliana Fabiana , Reis Alessandra , Pinho Vanessa , Barcelos Luciola , Santos Robson A S 
Published: November 2023

Recent studies advanced our understanding on the renin‐angiotensin system actions in the pathogenesis of several diseases. We now recognize angiotensin‐(1–7) [Ang‐(1–7)] as having pivotal role in antagonizing cell proliferation, tissue fibrosis and inflammation. We previously showed that Ang‐(1–7) attenuates chronic allergic lung inflammation and airway hyperresponssiveness. In this study, we investigated the effect of Ang‐(1–7) in the resolution of the allergic lung inflammatory response. Balb/c mice were randomly assigned to three groups: Control group; ovalbumin (OVA)‐sensitized and ‐challenged group; and ovalbumin‐sensitized and ‐challenged group treated with Ang‐(1–7). Sensitization was made by two injections of OVA (50 μg per mouse, i.p) in 2% aluminum hydroxide gel adjuvant at 7 days interval. On the 12nd day, sensitized mice received OVA challenge until 19th day (10 μg of OVA or PBS, intranasal). Ang‐(1–7) treatment (2μg/ mouse, v.o.) 24h after the last OVA challenge. Mice were killed by anesthetic overdose, 24h after Ang‐(1–7) treatment and bronchoalveolar lavage fluid (BALF) was made and next, lungs were collected. Morphometric analysis and determination of ERK1/2, IκB‐α and GATA3 by Western blotting were performed in the lung. Analysis of the number of inflammatory cells and immunofluorescence for Caspase 3 and NF‐κB were performed in the BALF. Efferocytosis assay was performed in different group of FVBN mice. Briefly, human neutrophil apoptotic cells were injected i.p. in zymosan‐induced peritonitis mice control or treated with Ang‐(1–7) (3μg). The peritoneal lavage was collected. Ang‐(1–7) promotes resolution of airway inflammation by induction apoptosis and inhibition of NF‐κB in eosinophils. Ang‐(1–7) also increased efferocytosis. In addition, treatment with Ang‐(1–7) reduced the GATA‐3, ERK1/2 and IκB‐α expression in lung of asthmatic animals and decrease pulmonary remodeling. Our results show that Ang‐(1–7) activates events that are crucial for the resolution of the inflammatory process and the return to homeostasis indicating Ang‐(1–7) as a novel endogenous pro‐resolving mediator. Support: FAPEMIG, CNPq, CAPES, INCT‐NanobiofarSupport or Funding InformationSupport: FAPEMIG, CNPq, CAPES, INCT‐Nanobiofar
Assessing cysteine residue thiol status in t‐Darpp, a protein involved in chemoresistance.
Authors: Aldana‐Mendoza Jesus Antonio , Farias Phillip , Momand Jamil Antonio 
Published: November 2023

The gene PPP1R1B expresses t‐Darpp, a protein that activates protein kinase A and the AKT pathway in breast cancer cells. t‐Darpp, when overexpressed in breast cancer cells, also confers resistance to trastuzumab, a therapeutic that binds to the Her2 receptor. Although t‐Darpp expression is relatively high in gastric, breast and colon cancers, its structure is unknown. Human t‐Darpp has two cysteine residues that can be exploited to explore t‐Darpp structure, Cys36 and Cys119. Methoxypolyethylene glycol‐maleimide (Mal‐PEG) was used to determine whether recombinant t‐Darpp cysteine thiols are on the surface of the protein and to find out if they are reversibly oxidized. This study shows that the two cysteine thiols are either buried or oxidized. Further work will be conducted to distinguish between these two possibilities.Support or Funding Informationthe NIH RISE program # GM 08101
The renal benzamil‐insensitive K+ excretion is independent of the BK channel
Authors: Jensen Iben Skov , Ruth Peter , Leipziger Jens Georg , Sørensen Mads Vaarby 
Published: November 2023

IntroductionTwo different secretory K+ channels are involved in the final homeostatic K+ excretion that takes place in the aldosterone‐sensitive distal nephron. One is the ROMK channel that co‐localizes with ENaC in the apical membrane of principal cells (PC) in the connecting tubule and collecting duct. PCs have a high expression of basolateral Na+/K+‐ATPase allowing for pump‐leak secretion of K+. K+ secretion via ROMK depends on Na+ reabsorption by ENaC to generate the necessary driving force.The BK (KCa1.1) channel is the other secretory pathway and is primarily found in the apical membrane of intercalated cells. The cellular mechanism of BK‐mediated K+ secretion is not fully understood. It is associated with flow‐induced K+ secretion (FIKS), since the kaliuretic response to increased flow is attenuated in KCNMA−/− (BK‐α knockout) mice as well as in IbTX treated tubules. Benzamil inhibits renal K+ excretion, however, leaving a blocker‐insensitive component intact. After chronic high K+ diet the benzamil‐insensitive renal K+ excretion is upregulated. In this project we asked, if the benzamil‐insensitive K+ excretion is mediated by the BK channel.MethodsThe benzamil‐sensitive and ‐insensitive kaliuresis was investigated in vivo in KCNMA+/+ and KCNMA−/− mice. This was performed on either control or high K+ (5 %) diet. Mice were pretreated with vehicle or benzamil and then received a volume‐load via gavage containing either control (sucrose 2%) or high K+ (2 %). Gavage increased diuresis and thus flow in the distal tubules. This is seen both with control gavage, where excess K+ excretion is unnecessary, and with K+ gavage that should naturally increase the need for K+ excretion.ResultsWe confirmed that benzamil attenuated, however, not completely abolished, urinary K+ excretion in all experiments. Hence, the K+ excretion could be divided into a benzamil‐sensitive and ‐insensitive fraction. The benzamil‐insensitive K+ excretion was upregulated by K+ loading, both acutely by K+ gavage but especially by chronic K+‐loading via high K+ diet. Importantly, we found no difference in the benzamil‐insensitive K+ excretion between KCNMA+/+ and KCNMA−/− mice in any of the investigated conditions.ConclusionOur data suggests (1) that K+ secretion via both ROMK and BK is highly dependent on ENaC activity and (2) that ROMK‐mediated K+ secretion compensates for the lack of BK‐mediated K+ secretion in KCNMA−/− mice. Furthermore (3), the benzamil‐insensitive K+ secretion appears independent of the BK channel and (4) is markedly regulated by both acute and chronic K+‐loading.
Multi‐Domain Dynamic Studies of Calcium Bound Polycystic Kidney Disease‐Like and Collagen Binding Domains
Authors: Ruth Christopher Eric , Sakon Joshua 
Published: November 2023

Clostridium histolyticum secretes at least two collagenases, ColH and ColG, that allow for degradation of extracellular matrices of animal tissue. C. histolyticum collagenases virulence factors are proposed to undergo domain rearrangement upon secretion from the bacteria to the host. In order to accomplish this, collagenases seek the least ordered regions in collagen to efficiently disassemble the fibril. Two types of domains, Polycystic Kidney Disease‐Like (PKD) and Collagen Binding Domain (CBD), direct the collagenases ability to disassemble the fibril. Calcium dependent structural change, increases in thermal stability, increases in efficiency for collagen binding, for individual domains, PKD and CBD, have been reported. Different surface properties and indications of varied dynamics suggest unique roles for the PKD‐like domains in ColG and in ColH. These domains are useful in anchoring fused growth factors to lesions. The multi‐domain dynamics have been found to be dependent on calcium concentrations. Most recent results show that use of multi‐domain targeting segments result in more efficacious preclinical outcomes in various animal models. Single domain targeting segments have been extensively reported, however multi‐domain targeting segments have not been biophysically characterized. In this presentation, Small Angle X‐Ray Scattering (SAXS) methods were used to monitor calcium dependent structural change of multi‐domain segments. All SAXS data were collected at 10°C through the Advanced Light Source at Berkley National Lab (SIBYLS beamline, 12.3.1). The average of 33 beam exposures were collected and processed through primusqt (ATSAS 2.6.1 software package). The bacteria evolved to take advantage of calcium concentration differential between inside the bacteria and the extracellular matrix to efficiently secrete virulence factors.Support or Funding InformationSupported by a grant from NIGMS (P20 GM103429) at NIH.
Surgical site infections in patients undergoing breast oncological surgery during the lockdown: An unexpected lesson from the COVID-19 pandemic
Authors: Cappelli Sonia , Corallino Diletta , Clementi Marco , Guadagni Stefano , Pelle Fabio , Puccica Ilaria , Barba Maddalena , Vici Patrizia , Sperduti Isabella , Costantini Maurizio , Botti Claudio 
Published: November 2023

Background:
The present study aims to evaluate how the measures to contain the SARS-CoV-2 spreading affected the surgical site infections (SSIs) rate in patients who underwent nondeferrable breast cancer surgery (BCS).

Methods:
This study is a retrospective analysis of prospectively collected data from a consecutive series of patients underwent nondeferrable BCS in a regional Italian Covid-free hub during two different period: March to April 2020 (pandemic cohort [PC]) and March till April 2019 (control cohort [CC]). SSIs were defined according to the criteria established by the Center for disease control and prevention (CDC) and additional treatment, serous discharge, erythema, purulent exudate, separation of deep tissues, isolation of bacteria, and stay (ASEPSIS) scoring systems.

Results:
One hundred ninety-nine patients were included in the present study: 100 and 99 patients who underwent nondeferrable BCS from March to April 2020 (PC) and from March to April 2019 (CC), respectively. The overall SSIs rate in this series was 9.1% according to CDC criteria and 6.5% according to ASEPSIS criteria. The SSIs incidence decreased during the pandemic period. Moreover, the SSIs rate according to ASEPSIS criteria was statistically lower in the PC than in the CC. We observed significant evidence of higher SSIs, both in terms of CDC and ASEPSIS score, in patients having undergone breast reconstruction compared with patients not undergoing immediate reconstruction.

Conclusions:
The restrictive measures issued during the lockdown period seemed to lower the SSIs rates in patients undergoing nondeferrable BCS.
Laparoscopic transanal total mesorectal excision (taTME) for rectal cancer
Authors: Conti Pietro , La Greca Giorgio , Muratore Andrea , Trombatore Giovanni 
Published: November 2023

Background:
Total mesorectal excision (TME) and multimodal approach have incredibly changed the long-term outcomes of the patients with mid-low rectal cancer. Open or laparoscopic transabdominal TME represents the gold-standard approach to rectal cancer. However, up-to-down TME is technically demanding, especially in male patients with narrow pelvis, in obese patients. The transanal total mesorectal excision (taTME) seems to exceed the limits of the laparoscopic TME.

Methods:
After a training made of courses, cadaver-labs, and proctored cases, we approached transanally patients with mild-low rectal cancer. Between 2015 and 2020, 33 patients with rectal cancer have undergone laparoscopic taTME procedure with a single-team approach. Aim of the present paper is to report our initial experience in term of short terms outcomes and histological results.

Results:
Thirty-three patients with rectal cancer were included in this study: 19 males (57.6%) and 14 females (42.4%). The median distance of the rectal cancer from anal verge was 6.5 cm. Overall, 23 patients (69.7%) underwent long-course neoadjuvant therapy. The overall morbidity rate was 36% (12 patients). Anastomotic leak occurred in two patients (6.2%) that required reoperation. Postoperative mortality was 3%. Specimen was graded as complete in 100% of patients. Circumferential resection margin (CRM) was in median 6.52 mm (range 4–18 mm).

Conclusion:
The taTME is a safe alternative to standard laparoscopic TME in selected patients with low rectal cancer. This technique which would seem to be feasible if performed by an experienced colorectal surgeon even if practiced in a suburban hospital.
NADPH oxidase-mediated sulfenylation of cysteine derivatives is key regulatory events for plant immune responses
Authors: Hino Yuta , Inada Taichi , Yoshioka Miki , Yoshioka Hirofumi 
Published: November 2023

AbstractReactive oxygen species (ROS) are rapidly generated during plant immune responses by RBOH, which is a plasma membrane-localizing NADPH oxidase. Although regulatory mechanisms of RBOH activity have been well documented, the ROS-mediated downstream signaling is unclear. We here demonstrated that ROS sensor proteins play a central role in the ROS signaling via oxidative post-translational modification of cysteine residues, sulfenylation. To detect protein sulfenylation, we used dimedone, which specifically and irreversibly binds to sulfenylated proteins. The sulfenylated proteins were labeled by dimedone inNicotiana benthamianaleaves, and the conjugates were detected by immunoblotting. In addition, a reductant dissociated H2O2-induced conjugates, suggesting that cysteine persulfide and/or polysulfides are involved in sulfenylation. Sulfenylation of cysteine and its derivatives in ROS sensor proteins were continuously increased during both PTI and ETI in an RBOH-dependent manner. Pharmacological inhibition of ROS sensor proteins by dimedone perturbated cell death, ROS accumulation induced by INF1 and MEK2DD, and defense against fungal pathogens. On the other hand, Rpi-blb2-mediated ETI responses were rather enhanced by dimedone. These results suggest that the sulfenylation of cysteine and its derivatives in various ROS sensor proteins are important events in downstream of RBOH-dependent ROS burst to regulate plant immune responses.HighlightNADPH oxidase-mediated ROS production induces sulfenylation of cysteine residues or their derivatives of ROS sensor proteins, which regulates HR cell death, ROS accumulation, and defense against diverse plant pathogens.
Developmental trajectories and differences in functional brain network properties of preterm and at-term neonates
Authors: López-Guerrero N , Alcauter S 
Published: November 2023

AbstractPremature infants, born before 37 weeks of gestation can have alterations in neurodevelopment and cognition, even when no anatomical lesions are evident. Resting-state functional neuroimaging of naturally sleeping babies has shown altered connectivity patterns, but there is limited evidence on the developmental trajectories of functional organization in preterm neonates. By using a large dataset (n=597) from the developing Human Connectome Project, we explored the differences in graph theory properties between at-term and preterm neonates at term-equivalent age, considering the age subgroups proposed by the World Health Organization for premature birth. Leveraging the longitudinal follow-up for some preterm participants, we characterized the developmental trajectories for preterm and at-term neonates. We found significant differences between groups in connectivity strength, clustering coefficient, characteristic path length and global efficiency. Specifically, at term-equivalent ages, higher connectivity, clustering coefficient and efficiency are identified for neonates born at later postmenstrual ages. Similarly, the characteristic path length showed the inverse pattern. These results were consistent for a variety of connectivity thresholds at both the global (whole brain) and local level (brain regions). The brain regions with the greatest differences between groups include primary sensory and motor regions and the precuneus which may relate to the risk factors for sensorimotor and behavioral deficits associated with premature birth. Our results also show non-linear developmental trajectories for premature neonates, but decreased integration and segregation even at term-equivalent age. Overall, our results confirm altered functional connectivity, integration and segregation properties of the premature brain despite showing rapid maturation after birth.
Well-Paired-Seq2: High-Throughput and High-Sensitivity Strategy for Characterizing Low RNA-Content Cell/Nucleus Transcriptomes
Authors: Yin Kun , Zhao Meijuan , Xu Yiling , Zheng Zhong , Huang Shanqing , Liang Dianyi , Dong He , Guo Ye , Lin Li , Song Jia , Zhang Huimin , Zheng Junhua , Zhu Zhi , Yang Chaoyong 
Published: November 2023

AbstractHigh-throughput single-cell RNA sequencing (scRNA-seq) is recognized as a powerful technology for disentangling the heterogeneity of cellular states. However, the Poisson-dependent cell capture and low sensitivity in scRNA-seq methods pose challenges for throughput and for samples with low RNA-content. Herein, to address these challenges, we developed Well-Paired-Seq2 (WPS2) based on size-exclusion and locally quasi-static hydrodynamic principles to realize high efficiency of cell utilization, single cell/bead pairing, and cell-free RNA removal. WPS2 exploits molecular crowding effect, tailing activity enhancement in reverse transcription, and homogeneous enzymatic reaction in the initial bead-based amplification to achieve 3116 genes and 8447 transcripts. With an average of ∼20,000 reads per cell, WPS2 detected 1420 more genes and 4864 more transcripts than our previous Well-Paired-Seq. Using WPS2, we overcame the Poisson limit for the capture of both cells and beads and accurately characterized transcriptomes of low RNA-content single cells and nuclei with high sensitivity. WPS2 was further applied to comprehensively profile transcriptomes from frozen clinical samples. We found that clear cell renal cell carcinoma (ccRCC) has a complex microenvironment, and that chromophobe renal cell carcinoma (chRCC) exhibits abundant copy number variations (CNVs). In addition, metanephric adenoma (MA) was characterized at single-cell level for the first time and some potentially specific markers were revealed. With the advantages of high sensitivity, high throughput, and high fidelity, we anticipate that WPS2 will be broadly applicable in basic and clinical research.
Evaluating the performance of protein structure prediction in detecting structural changes of pathogenic nonsynonymous single nucleotide variants
Authors: Lai Hong-Sheng , Chen Chien-Yu 
Published: November 2023

AbstractProtein structure prediction serves as an efficient tool, saving time and circumventing the need for laborious experimental endeavors. Distinguished methodologies, including AlphaFold, RoseTTAFold, and ESMFold, have proven their precision through rigorous evaluation based on the last Critical Assessment of Protein Structure Prediction (CASP14). The success of protein structure prediction raises the following question: can the prediction tools discern structural alterations resulting from single amino acid changes? In this regard, the objective of this study is to assess the performance of existing structure prediction tools on mutated sequences. In this study, we posited that a specific fraction of the pathogenic nonsynonymous single nucleotide variants (nsSNVs) would experience structural alterations following amino acid mutations. We meticulously assembled an extensive dataset by initially sourcing data from ClinVar and subsequently applying multiple filters, resulting in 964 alternative sequences and their corresponding reference sequences. Utilizing UniProt, we acquired reference sequences and generated the corresponding alternative sequences based on variant information. This study performed three tools of structure prediction on both the reference and alternative sequences and expected some structural changes upon mutations. Our findings affirm AlphaFold as the foremost prediction tool presently; nonetheless, our experimental results underscore persistent challenges in accurately predicting structural alterations induced by nsSNVs. Discrepancies between the predicted structures of reference and alternative sequences, when observed, often stem from a lack of confidence in the predictions or the spatial separation between compact domains interrupted by disordered regions, posing challenges to successful alignment.
Formation of recurring transient Ca2+-based intercellular communities duringDrosophilahematopoiesis
Authors: David Saar Ben , Ho Kevin Y.L. , Tanentzapf Guy , Zaritsky Assaf 
Published: November 2023

AbstractTissue development occurs through a complex interplay between many individual cells. Yet, the fundamental question of how collective tissue behavior emerges from heterogeneous and noisy information processing and transfer at the single-cell level remains unknown. Here, we reveal that tissue scale signaling regulation can arise from local gap-junction mediated cell-cell signaling through the spatiotemporal establishment of an intermediate-scale of transient multicellular communication communities over the course of tissue development. We demonstrated this intermediate scale of emergent signaling using Ca2+signaling in the intact, ex vivo cultured, live developingDrosophilahematopoietic organ, the Lymph Gland (LG). Recurrent activation of these transient signaling communities defined self-organized signaling “hotspots” that receive and transmit information to facilitate repetitive interactions with non-hotspot neighbors, transfer information across cells, and regulate the developmental progression of hotspots. Overall, this work bridges the scales between single-cell and emergent group behavior providing key mechanistic insight into how cells establish tissue-scale communication networks.Significance statementCells coordinate their internal state and behavior by exchanging information with other cells in their vicinity. These local interactions are integrated across space and time to enable synchronized function at the tissue scale. Using live microscopy imaging of theDrosophilaLymph Gland, and by applying computational analyses, we identified and characterized a new mode of cellular communication through self-organized recurring coordinated short-term activation at the intermediate scale of 3-8 cells, which we call “hotspots”. We reveal that hotspots form over the course of tissue development, and are dependent on specific proteins, called gap-junctions, that enable communication between adjacent cells. Hotspots repeatedly transmit and retrieve information to and from their non-hotspot neighbors to spread information throughout the tissue to regulate and coordinate tissue function.
Influence of rifampicin-resistance mutations on the synthesis of antioxidant, DNA-protective, and SOS-inhibitory metabolites
Authors: Statsenko V.N. , Prazdnova E.V. 
Published: November 2023

AbstractThis work is aimed at studying the effects of rifampicin resistance mutations on the synthesis of secondary metabolites with antioxidant and DNA-protective properties.We used probiotic strains of the genusBacillus:B. amyloliquefaciensB-1895 andB. subtilisKATMIRA1933.The antioxidant, DNA-protective activity, and the ability to suppress the SOS-response inB. amyloliquefaciensB-1895 andB. subtilisKATMIRA1933 rifampicin-resistant mutants have been studied for the first time. It has been found that antioxidant, DNA protective, and SOS-inhibiting activity is higher in rifampicin-resistant mutants than that of original strains.According to the study results, it has been discovered that the antioxidant, DNA-protective and SOS-inhibitory activity in mutantsB. amyloliquefaciensB-1895 andB. subtilisKATMIRA1933 resistant to rifampicin is higher than in control strains, which indirectly proves the pleiotropic effect of therpoBgene on these activities.