bluuebunny/crossref_metadata_2025_split huggingface dataset:
In-silicoevaluation of Mirror repeats in some selected genes ofCandida albicans
Authors: Sehrawat Barkha , Yadav Priya , Sarjeet Mustak , Yadav Sakshi , Yadav Vidhi , Goyal Nupur , Alam Parvej , Ahlawat Meghali , Yadav Sandeep 
Published: January 2024

AbstractAll cellular processes in a living cell are controlled by its genetic material. DNA in majority of the domains acts as a regulatory molecule by controlling various vital functions. The genetic makeup of DNA or RNA (in viruses) is unique in all the domains. Their uniqueness is determined by the presence of various types of repetitive patterns of bases. These includes inverted repeats, tandem repeats, VNTR’s, palindromes etc. Among many repetitive pattern types, Mirror repeats (MR) found to be dispersed throughout the genes or genomes. These sequences are associated with various functional features like their involvement in H-DNA formation, in replication & transcription, nervous system related diseases development etc. The major focus of this investigation is to identify MR sequences from some selected genes ofCandida albicansusing a bioinformatics based pipeline. The approach refers to as FPCB which utilized some manual steps to extract out MR sequence from any targeted gene or genome. The current study find out that the identified Mirror repeats found to be dispersed throughout the selected genes along with variable length. Among them the maximum & minimum MR sequences were reported in the gene FAS2 (108) & HIS1 (15) respectively. The present study will be helpful to provide a new insight for molecular as well as computational based studies ofCandida albicansas well as other related fungal groups.
Characterization of a Unique Spontaneous Calcifying Cell Line (CJ): a Novel Tool for the Study of Ectopic Calcification
Authors: Ida Nobutaka , Yamane Yoshihisa 
Published: January 2024

AbstractPurposeDue to the lack of an appropriate in vitro evaluation system, there is no effective prevention or treatment for ectopic calcification diseases (ECD). We obtained canine renal adenocarcinoma cells (CJ cells) that spontaneously form large amounts of calcified precipitates (CaP-ppt) and examined whether they could serve as a model for the early stages of ectopic calcification (EC).MethodsDispersed cells obtained by collagenase-DNase digestion were cultured in 10% FBS, antibiotic-containing DMEM-high glucose medium (standard medium). CaP-ppt was stained with Alizarin Red (AR) and colorimetrically quantified after acid extraction. Cell volume was determined by Crystal violet (CV) staining followed by extraction and colorimetric quantification. Calcium (Ca) and phosphate (PO4) were determined with a commercial kit to obtain the Ca/P ratio. Screening of anti-CaP-ppt compounds was performed in the same 96-well plate in the order of cell culture ⇒ CaP-ppt quantification ⇒ cell quantification and evaluated by IC50value.ResultsCJ cells produced large amounts of CaP-ppt on standard medium alone without external phosphate addition; CaP-ppt formation was not accompanied by cell death, but on the contrary, CaP-ppt increased at physiological pH values around pH 7.4 due to active cell metabolism. The Ca2+and PO43-partitioning kinetics to CaP-ppt were found, and the Ca/P ratio of CaP-ppt was stable at 1.35. The anti-Cap-ppt effects of bisphosphonates and all-trans retinoic acid (ATRA) were also confirmed in this CJ cell CaP-ppt system.DiscussionThere was doubt about the vascular calcifying cell model with the addition of high concentrations of phosphoric acid, but there were no suitable alternative cells. Spontaneously calcifying CJ cells provide a fundamental solution to this problem. Anti-CaP-ppt screening also eliminates the need for medium exchange, thus saving labor and cost. The Ca/P ratio of CaP-ppt in CJ cells is 1.35, the same as that of amorphous Ca phosphate (ACP), corresponding to the early (reversible) stage of EC. Therefore, it has favorable conditions as an evaluation system for drug discovery.ConclusionCJ cells, which calcify at physiological phosphate concentrations (0.9 mM) in standard media, are useful and novel research material for basic and preventive studies of ECD and for drug development studies.
A weighted and cumulative point system for accurate scoring of intestinal pathology in a piglet model of necrotizing enterocolitis
Authors: Offersen Simone Margaard , Henriksen Nicole Lind , Brunse Anders 
Published: January 2024

AbstractBackgroundNecrotizing enterocolitis (NEC) is a serious condition, primarily affecting premature infants, in which a portion of the gut undergoes inflammation and necrosis. Symptoms of NEC are unspecific, and together with a rapid progression, the disease remains a significant concern. The preterm pig develops NEC spontaneously, making it a suitable model for exploring novel treatments. During piglet necropsy, NEC-lesions closely resemble the pathologies found during surgery or autopsy of preterm infants. As such, the systematic gross inspection enables direct evaluation of gut lesions, which is not possible in the medical preterm patient. Here, we introduce a revised intestinal scoring system with an expanded score range and more detailed descriptive features to accurately describe the diversity of NEC-lesions in the preterm piglet model.MethodsWe included 333 preterm piglets from four separate experiments, each delivered via cesarian section at 90% gestation. The pigs were fed either a gently processed (GP) or harshly processed (HP) milk formula for 96 hours and were subsequently euthanized. At necropsy, the gastrointestinal tract was assessed with 1) an established 6-grade scoring system and 2) a systematic and descriptive approach focusing on the distribution and severity of hyperemia, hemorrhage, pneumatosis intestinalis (intramural gas), and necrosis. Lesion biopsies were sampled for cytokine measurement and a subset (n= 62) was sampled for histopathological assessment.ResultsThe systematic and descriptive registrations were evaluated and converted into a weighted and cumulative point (WCP) score. Compared to the 6-grade score, the WCP score enabled a higher discrepancy in severity levels, especially among organs with more prominent NEC lesions. IL-1β in small intestinal lesions and both IL-8 and IL-1β in colon lesions correlated positively with the WCP scale. A histopathological grade system (0-8) was established and revealed mucosal lesions not recognized macroscopically. Finally, the WCP score showed a higher NEC-promoting effect of the HP formula compared to the GP formula.ConclusionThe validation of the weighted and cumulative scoring system demonstrated an expanded score range, enhancing the accuracy in describing NEC-lesions in gastrointestinal segments of preterm pigs. This approach may increase the efficiency of preclinical NEC experiments.
CRISPR-repressed toxin-antitoxin provides population-level immunity against diverse anti-CRISPR elements
Authors: Shu Xian , Wang Rui , Li Zhihua , Xue Qiong , Wang Jiajun , Liu Jingfang , Cheng Feiyue , Liu Chao , Zhao Huiwei , Hu Chunyi , Li Jie , Ouyang Songying , Li Ming 
Published: January 2024

ABSTRACTProkaryotic CRISPR-Cas systems are highly vulnerable to phage-encoded anti-CRISPR (Acr) factors. How CRISPR-Cas systems protect themselves remains unclear. Here, we uncovered a broad-spectrum anti-anti-CRISPR strategy involving a phage-derived toxic protein. Transcription of this toxin is normally reppressed by the CRISPR-Cas effector, but is activated to halt cell division when the effector is inhibited by any anti-CRISPR proteins or RNAs. We showed that this abortive infection-like effect efficiently expels Acr elements from bacterial population. Furthermore, we exploited this anti-anti-CRISPR mechanism to develop a screening method for specific Acr candidates for a CRISPR-Cas system, and successfully identified two distinct Acr proteins that enhance the binding of CRISPR effector to non-target DNA. Our data highlight the broad-spectrum role of CRISPR-repressed toxins in counteracting various types of Acr factors, which illuminates that the regulatory function of CRISPR-Cas confers host cells herd immunity against Acr-encoding genetic invaders, no matter they are CRISPR-targeted or not.
Investigating thecis-Regulatory Basis of C3and C4Photosynthesis in Grasses at Single-Cell Resolution
Authors: Mendieta John Pablo , Tu Xiaoyu , Jiang Daiquan , Yan Haidong , Zhang Xuan , Marand Alexandre P. , Zhong Silin , Schmitz Robert J. 
Published: January 2024

AbstractWhile considerable knowledge exists about the enzymes pivotal for C4photosynthesis, much less is known about thecis-regulation important for specifying their expression in distinct cell types. Here, we use single-cell-indexed ATAC-seq to identify cell-type-specific accessible chromatin regions (ACRs) associated with C4enzymes for five different grass species. This study spans four C4species, covering three distinct photosynthetic subtypes:Zea maysandSorghum bicolor(NADP-ME),Panicum miliaceum(NAD-ME),Urochloa fusca(PEPCK), along with the C3outgroupOryza sativa. We studied thecis-regulatory landscape of enzymes essential across all C4species and those unique to C4subtypes, measuring cell-type-specific biases for C4enzymes using chromatin accessibility data. Integrating these data with phylogenetics revealed diverse co-option of gene family members between species, showcasing the various paths of C4evolution. Besides promoter proximal ACRs, we found that, on average, C4genes have two to three distal cell-type-specific ACRs, highlighting the complexity and divergent nature of C4evolution. Examining the evolutionary history of these cell-type-specific ACRs revealed a spectrum of conserved and novel ACRs, even among closely related species, indicating ongoing evolution ofcis-regulation at these C4loci. This study illuminates the dynamic and complex nature of CRE evolution in C4photosynthesis, particularly highlighting the intricatecis-regulatory evolution of key loci. Our findings offer a valuable resource for future investigations, potentially aiding in the optimization of C3crop performance under changing climatic conditions.
Joint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone
Authors: Ellis Thomas James , Field David Luke , Barton Nicholas H. 
Published: January 2024

1AbstractThe distribution of pollen dispersal distances sets the scale for plant population dynamics. A useful approach for inferring the distribution dispersal distances is to infer the distances between mates by paternity or parentage reconstruction. This is most powerful when information about multiple properties or data types are inferred in a joint analysis. We describe an approach to jointly infer paternity, sibling relationships and population parameters, with the example of the pollen dispersal kernel in a natural population of the yellow-floweredAntirrhinum majus striatumand the magenta-floweredA. m. pseudomajus. Pollen dispersal is lep-tokurtic, with half of mating events occurring within 30m, but with a long tail of mating events up to 747m. We also find tentative evidence that fathers tend to be to the East of mothers, indicating that there is a bias in pollen dispersal fromA. m. pseudomajusintoJoint estimation of paternity, sibships and pollen dispersal in a snapdragon hybrid zone A. m. striatum. The scale of pollen dispersal is large enough that pollinators should encounter the full range of hybrid phenotypes in the hybrid zone, and would be sufficient for any pollinator-mediated selection to influence male or female fitness.
A limited concentration range of diaphorin, a polyketide produced by a bacterial symbiont of the Asian citrus psyllid, promotes thein vitrogene expression with bacterial ribosomes
Authors: Takasu Rena , Izu Takashi , Nakabachi Atsushi 
Published: January 2024

AbstractDiaphorin is a polyketide produced by “CandidatusProfftella armatura” (Gammaproteobacteria:Burkholderiales), an obligate symbiont of a devastating agricultural pest, the Asian citrus psyllidDiaphorina citri(Hemiptera: Psyllidae). Physiological concentrations of diaphorin, whichD. citricontains at levels as high as 2–20 mM, are inhibitory to various eukaryotes andBacillus subtilis(Firmicutes:Bacilli) but promote the growth and metabolic activity ofEscherichia coli(Gammaproteobacteria:Enterobacterales). Our previous study demonstrated that five-millimolar diaphorin, which exhibits significant inhibitory and promoting effects on culturedB. subtilisandE. coli, respectively, inhibitsin vitrogene expression utilizing purifiedB. subtilisandE. coliribosomes. This suggested that the adverse effects of diaphorin onB. subtilisare partly due to its influence on gene expression. However, the result appeared inconsistent with the positive effects onE. coli. Moreover, the diaphorin concentration in bacterial cells, where genes are expressedin vivo, may be lower than in culture media. Therefore, the present study analyzed the effects of 50 and 500 μM of diaphorin on bacterial gene expression using the same analytical method. The result revealed that this concentration range of diaphorin, in contrast to five-millimolar diaphorin, promotes thein vitrotranslation with theB. subtilisandE. coliribosomes, suggesting that the positive effects of diaphorin onE. coliare due to its direct effects on translation. This study demonstrated for the first time that a pederin-type compound promotes gene expression, establishing a basis for utilizing its potential in pest management and industrial applications.ImportanceThis study revealed that a limited concentration range of diaphorin, a secondary metabolite produced by a bacterial symbiont of an agricultural pest, promotes cell-free gene expression utilizing substrates and proteins purified from bacteria. The unique property of diaphorin, which is inhibitory to various eukaryotes andBacillus subtilisbut promotes the growth and metabolic activity ofEscherichia coli, may affect the microbial flora of the pest insect, potentially influencing the transmission of devastating plant pathogens. Moreover, the activity may be exploited to improve the efficacy of industrial production byE. coli, which is often used to produce various important materials, including pharmaceuticals, enzymes, amino acids, and biofuels. This study elucidated a part of the mechanism by which the unique activity of diaphorin is expressed, constructing a foundation for applying the unique property to pest management and industrial use.
Human cell surface-AAV interactomes identify LRP6 as blood-brain-barrier transcytosis receptor and immune cytokine IL3 as AAV9 binder
Authors: Shay Timothy F. , Jang Seongmin , Chen Xinhong , Walker Beth , Tebbutt Claire , Wolfe Damien A. , Brittain Tyler J. , Arokiaraj Cynthia M. , Sullivan Erin E. , Ding Xiaozhe , Wang Ting-Yu , Lei Yaping , Chuapoco Miguel R. , Chou Tsui-Fen , Gradinaru Viviana 
Published: January 2024

AbstractAdeno-associated viruses (AAVs) are foundational gene delivery tools for basic science and clinical therapeutics. However, lack of mechanistic insight, especially for engineered vectors created by directed evolution, can hamper their application. Here, we adapted an unbiased human cell microarray platform to determine the extracellular and cell surface interactomes of natural and engineered AAVs. We identified a naturally-evolved and serotype-specific interaction between the AAV9 capsid and human interleukin 3 (IL3), with possible roles in host immune modulation, as well as lab-evolved low-density-lipoprotein-receptor-related-protein 6 (LRP6) interactions specific to engineered capsids that cross the blood-brain barrier in non-human primates after intravenous administration. The unbiased cell microarray screening approach also allowed us to identify off-target tissue binding interactions of engineered brain-enriched AAV capsids that may inform vectors’ peripheral organ tropism and side effects. These results allow confident application of engineered AAVs in diverse organisms and unlock future target-informed engineering of improved viral and non-viral vectors for non-invasive therapeutic delivery to the brain.
GENOMIC PROFILING OF SARS-COV-2 STRAINS CIRCULATING IN SOUTH EASTERN REGION OF INDIA DURING THREE WAVES OF PANDEMIC
Authors: Kandhasamy Vanathy , Balakrishna Pillai Agieshkumar , Mariappan Vignesh , Ramalingam Malarvizhi , Raganadin Pajanivel , Ramadoss Ramya , Moovarkumudalvan Balasubramanian , Easow Joshy M , Vasudevan Madavan , S.R. Rao 
Published: January 2024

AbstractContinuous bio-surveillance of SARS-CoV-2 is an ongoing task at local, national and global levels since the pandemic onset for understanding genetic evolution and vaccine efficacy. Present study was designed to track the emergence of new variants along the duration of three peaks of infection in the city of Puducherry, India. A total of 128 samples were subjected to Illumina deep RNA sequencing. The results showed predominance of uncommon, delta and omicron variants in first, second and third waves respectively. The most common pangolin lineage was B.1.560 and B.1.617.2. The study observed a total of 3133 common and 11 new mutations. The most common is in the Spike_D614G. A new set of mutations was observed in key viral factors such as NS16 that are implicated to be involved in immune evasion. This may have impact on enhanced disease virulence, vaccine efficiency and possible tolerance to current antivirals. This warrants further in vitro studies to understand the significance of the mutations. While the results presented would also augment the ongoing research on evolutionary and the genetic epidemiology of SARS-CoV-2, it also emphasizes the need for continuous genetic monitoring to predict the forthcoming threats due to the emergence of new or existing variants.
A new story of four Hexapoda classes: Protura as the sister to all other hexapods
Authors: Du Shiyu , Tihelka Erik , Yu Daoyuan , Chen Wan-Jun , Bu Yun , Cai Chenyang , Engel Michael S. , Luan Yun-Xia , Zhang Feng 
Published: January 2024

SUMMARYInsects represent the most diverse animal group, yet previous phylogenetic analyses based on the morphological and molecular data have failed to agree on the evolutionary relationships of early insects and their six-legged relatives (together constituting the clade Hexapoda). In particular, the phylogenetic positions of the three early-diverging hexapod groups, the coneheads (Protura), springtails (Collembola), and two-pronged bristletails (Diplura), have been debated for over a century, with alternative topologies implying drastically different scenarios of the evolution of the insect body plan and hexapod terrestrialisation. We addressed this issue by sampling of all hexapod orders, and experimented with a broad range of across-site compositional heterogeneous models designed to tackle ancient divergences. Our analyses support Protura as the earliest-diverging hexapod lineage (Protura-sister) and Collembola as a sister group to the Diplura, a clade we refer to as ‘Antennomusculata’ characterised by the shared possession of internal muscles in the antennal flagellum. The universally recognized ‘Ellipura’ hypothesis is recovered under the site-homogenous LG model. Our cross-validation analysis shows that the CAT-GTR model that recovers Protura-sister fits significantly better than homogenous model. Furthermore, as a very unusual group, Protura as the first diverging lineage of hexapods is also supported by other lines of evidence, such as mitogenomics, comparative embryology, and sperm morphology. The backbone phylogeny of hexapods recovered in this study will facilitate the exploration of the underpinnings of hexapod terrestrialisation and mega-diversity.
Direct excitatory synapses between neurons and tumor cells drive brain metastatic seeding of breast cancer and melanoma
Authors: Venkataramani V. , Karreman M.A. , Nguyen L.C. , Tehranian C. , Hebach N. , Mayer C.D. , Meyer L. , Mughal S.S. , Reifenberger G. , Felsberg J. , Köhrer K. , Schubert M.C. , Westphal D. , Breckwoldt M.O. , Brors B. , Wick W. , Kuner T. , Winkler F. 
Published: January 2024

AbstractInteractions between neurons and cancer cells are found in many malignancies, but their relevance for metastatic organ colonization remain largely unknown. It is also unclear whether any direct synaptic communication between neurons and cancer cells of non-neural tumor types exists, and if so, whether this can support metastasis and thus cancer progression. Here we show that excitatory synapses are formed between neurons and brain-metastatic melanoma and breast cancer cells. This starts at an early microscopic stage after extravasation into the brain parenchyma, during residence of cancer cells in the perivascular niche, a critical step for their survival. These neuron-cancer synapses showed abona fidesynaptic ultrastructure, and generated excitatory postsynaptic currents mediated by glutamate receptors of the AMPA subtype in cancer cells. In accordance, AMPA receptor signatures were consistently detected in preclinical and patient samples of melanoma and breast cancer brain metastases. Genetic perturbation and pharmacological inhibition of AMPA receptors with the approved antiepileptic drug perampanel in models of breast and melanoma cancer reduced the number of brain metastases and overall brain metastatic burden. These findings demonstrate for the first time that neurons can form biologically relevant direct synapses with non-neural cancer cells. In brain metastasis, a particularly challenging complication of many common malignancies, this non-canonical stimulatory synaptic interaction offers novel therapeutic opportunities.
Engineering of methionine-auxotrophEscherichia colivia parallel evolution of two enzymes fromCorynebacterium glutamicum’sdirect-sulfurylation pathway enables its recovery in minimal medium
Authors: Gabay Matan , Stern Inbar , Gruzdev Nadya , Cohen Adi , Lifshits Lucia Adriana , Ansbacher Tamar , Yadid Itamar , Gal Maayan 
Published: January 2024

AbstractMethionine biosynthesis relies on the sequential catalysis of multiple enzymes.Escherichia coli, the main bacteria used in research and industry for protein production and engineering, utilizes the three-step trans-sulfurylation pathway catalyzed by L-homoserine O-succinyl transferase, cystathionine gamma synthase and cystathionine beta lyase to convert L-homoserine to L-homocysteine. However, most bacteria employ the two-step direct-sulfurylation pathway involving L-homoserine O-acetyltransferases and O-acetyl homoserine sulfhydrylase. We previously showed that a methionine-auxotrophE. colistrain (MG1655) with deletion of metA, encoding for L-homoserine O-succinyl transferase, and metB, encoding for cystathionine gamma synthase, could be complemented by introducing the genes metX, encoding for L-homoserine O-acetyltransferases and metY, encoding for O-acetyl homoserine sulfhydrylase, from various sources, thus altering theEscherichia colimethionine biosynthesis metabolic pathway to direct-sulfurylation. However, introducing metX and metY fromCorynebacterium glutamicumfailed to complement methionine auxotrophy. Herein, we generated a randomized genetic library based on the metX and metY ofCorynebacterium glutamicumand transformed it into a methionine-auxotrophicE. colistrain lacking the metA and metB genes. Through multiple enrichment cycles, we successfully isolated active clones capable of growing in M9 minimal media without external methionine supplementation. The dominant metX mutations in the evolved methionine-autotrophsEscherichia coliwere L315P and H46R. Interestingly, we found that a metY gene encoding only the N-terminus 106 out of 438 amino acids of the wild-type MetY enzyme is functional and supports the growth of the methionine auxotroph. Recloning the new genes into the original plasmid and transforming them to methionine auxotrophEscherichia colivalidated their functionality. These results show that directed enzyme-evolution enables the fast engineering of new active variants within theEscherichia colimethionine direct-sulfurylation pathway, leading to efficient complementation.