bluuebunny/crossref_metadata_2025 huggingface dataset:
A new chromosome-scale genome of wild Brassica oleracea provides insights into the domestication of Brassica crops
Authors: Ji Gaoxiang , Long Ying , Cai Guangqin , Wang Aihua , Yan Guixin , Li Hao , Gao Guizhen , Xu Kun , Huang Qian , Chen Biyun , Li Lixia , Li Feng , Nishio Takeshi , Shen Jinxiong , Wu Xiaoming
Published: February 2024

The cultivated diploid Brassica oleracea is an important vegetable crop, but the genetic basis of its domestication remains largely unclear in the absence of high-quality reference genomes of wild B. oleracea. Here, we report the first chromosome-level assembly of the wild Brassica oleracea L. W03 genome (total genome size, 630.7 Mb; scaffold N50, 64.6 Mb). Using the newly assembled W03 genome, we constructed a gene-based B. oleracea pangenome and identified 29 744 core genes, 23 306 dispensable genes, and 1896 private genes. We re-sequenced 53 accessions, representing six potential wild B. oleracea progenitor species. The results of the population genomic analysis showed that the wild B. oleracea populations had the highest level of diversity and represents the most closely related population to modern-day horticultural B. oleracea. In addition, the WUSCHEL gene was found to play a decisive role in domestication and to be involved in cauliflower and broccoli curd formation. We also illustrate the loss of disease-resistance genes during selection for domestication. Our results provide new insights into the domestication of B. oleracea and will facilitate the future genetic improvement of Brassica crops.
Chromatin sensing: integration of environmental signals to reprogram plant development through chromatin regulators
Authors: Wang Wenli , Sung Sibum
Published: February 2024

Chromatin regulation in eukaryotes plays pivotal roles in controlling the developmental regulatory gene network. This review explores the intricate interplay between chromatin regulators and environmental signals, elucidating their roles in shaping plant development. As sessile organisms, plants have evolved sophisticated mechanisms to perceive and respond to environmental cues, orchestrating developmental programs that ensure adaptability and survival. A central aspect of this dynamic response lies in the modulation of versatile gene regulatory networks, mediated in part by various chromatin regulators. Here, we summarized current understanding of the molecular mechanisms through which chromatin regulators integrate environmental signals, influencing key aspects of plant development.
A clinical update of compound heterozygosity for hemoglobin Hekinan II [a27(B8)Glu–Asp; HBA1: c.84G>T] variant in China
Authors: Pan Liqiu , Qiu Yuling , Ye Lihua , Li Linlin , Huang Yuanyuan , Mo Wuning , Lin Faquan
Published: February 2024

Background

Hemoglobin (Hb) Hekinan II (A27; Glu-Asp) is an α-chain variant, and its interaction with the common Southeast Asian (--SEA/) α-thalassemia (α-thal) deletion is rarely reported. This study provides a clinical update of Hb Hekinan II associated with (--SEA/) α-thal.

Methods

A total of 11 simple heterozygotes and 20 composite heterozygotes for Hb Hekinan II and (--SEA/) α-thal were included based on molecular diagnosis.

Results

Hb Hekinan II exhibited a significant increase in hemoglobin, mean corpuscular volume, and mean corpuscular hemoglobin content, but a decrease in red blood cell level compared with α+ thalassemia deletion. Compared with (--SEA/) α-thal, composite heterozygotes for Hb Hekinan II and (--SEA/) α-thal showed similar erythrocyte parameters. Both heterozygotes with and without (--SEA/) α-thal showed low Hb A2 level. Hb Hekinan II showed abnormal performance in high-performance liquid chromatography but not in capillary electrophoresis.

Conclusion

Hb Hekinan II is a benign Hb variant. The heterozygotes exhibit clinically asymptomatic coinheritance with (--SEA/) α-thal having comparable hematological phenotype to simple (--SEA/) α-thal. The combination of hematological and molecular analysis helped to improve the detection rate of this rare variant.
Myokines: metabolic regulation in obesity and type 2 diabetes
Authors: Chen Zhi-Tian , Weng Zhi-Xuan , Lin Jiandie D , Meng Zhuo-Xian
Published: February 2024

Skeletal muscle plays a vital role in the regulation of systemic metabolism, partly through its secretion of endocrine factors which are collectively known as myokines. Altered myokine levels are associated with metabolic diseases, such as type 2 diabetes (T2D). The significance of interorgan crosstalk, particularly through myokines, has emerged as a fundamental aspect of nutrient and energy homeostasis. However, a comprehensive understanding of myokine biology in the setting of obesity and T2D remains a major challenge. In this review, we discuss the regulation and biological functions of key myokines that have been extensively studied during the past two decades, namely interleukin 6 (IL-6), irisin, myostatin (MSTN), growth differentiation factor 11 (GDF11), fibroblast growth factor 21 (FGF21), apelin, brain-derived neurotrophic factor (BDNF), meteorin-like (Metrnl), secreted protein acidic and rich in cysteine (SPARC), β-aminoisobutyric acid (BAIBA), Musclin, and Dickkopf 3 (Dkk3). Related to these, we detail the role of exercise in myokine expression and secretion together with their contributions to metabolic physiology and disease. Despite significant advancements in myokine research, many myokines remain challenging to measure accurately and investigate thoroughly. Hence, new research techniques and detection methods should be developed and rigorously tested. Therefore, developing a comprehensive perspective on myokine biology is crucial, as this will likely offer new insights into the pathophysiological mechanisms underlying obesity and T2D and may reveal novel targets for therapeutic interventions.
Formation of Different Polyploids Through Disrupting Meiotic Crossover Frequencies Based oncntd1Knockout in Zebrafish
Authors: Ou Yuan , Li Huilin , Li Juan , Dai Xiangyan , He Jiaxin , Wang Shi , Liu Qingfeng , Yang Conghui , Wang Jing , Zhao Rurong , Yin Zhan , Shu Yuqin , Liu Shaojun
Published: February 2024

Polyploidy, a significant catalyst for speciation and evolutionary processes in both plant and animal kingdoms, has been recognized for a long time. However, the exact molecular mechanism that leads to polyploid formation, especially in vertebrates, is not fully understood. Our study aimed to elucidate this phenomenon using the zebrafish model. We successfully achieved an effective knockout of the cyclin N-terminal domain containing 1 (cntd1) using CRISPR/Cas9 technology. This resulted in impaired formation of meiotic crossovers, leading to cell-cycle arrest during meiotic metaphase and triggering apoptosis of spermatocytes in the testes. Despite these defects, the mutant (cntd1−/−) males were still able to produce a limited amount of sperm with normal ploidy and function. Interestingly, in the mutant females, it was the ploidy not the capacity of egg production that was altered. This resulted in the production of haploid, aneuploid, and unreduced gametes. This alteration enabled us to successfully obtain triploid and tetraploid zebrafish from cntd1−/− and cntd1−/−/− females, respectively. Furthermore, the tetraploid-heterozygous zebrafish produced reduced-diploid gametes and yielded all-triploid or all-tetraploid offspring when crossed with wild-type (WT) or tetraploid zebrafish, respectively. Collectively, our findings provide direct evidence supporting the crucial role of meiotic crossover defects in the process of polyploidization. This is particularly evident in the generation of unreduced eggs in fish and, potentially, other vertebrate species.
The repertoire and structure of adhesion GPCR transcript variants assembled from publicly available deep-sequenced human samples
Authors: Kuhn Christina Katharina , Stenzel Udo , Berndt Sandra , Liebscher Ines , Schöneberg Torsten , Horn Susanne
Published: February 2024

Alternative splicing and multiple transcription start and termination sites can produce a diverse repertoire of mRNA transcript variants from a given gene. While the full picture of the human transcriptome is still incomplete, publicly available RNA datasets have enabled the assembly of transcripts. Using publicly available deep sequencing data from 927 human samples across 48 tissues, we quantified known and new transcript variants, provide an interactive, browser-based application Splice-O-Mat and demonstrate its relevance using adhesion G protein-coupled receptors (aGPCRs) as an example. On average, 24 different transcript variants were detected for each of the 33 human aGPCR genes, and several dominant transcript variants were not yet annotated. Variable transcription starts and complex exon-intron structures encode a flexible protein domain architecture of the N- and C termini and the seven-transmembrane helix domain (7TMD). Notably, we discovered the first GPCR (ADGRG7/GPR128) with eight transmembrane helices. Both the N- and C terminus of this aGPCR were intracellularly oriented, anchoring the N terminus in the plasma membrane. Moreover, the assessment of tissue-specific transcript variants, also for other gene classes, in our application may change the evaluation of disease-causing mutations, as their position in different transcript variants may explain tissue-specific phenotypes.
Peptide nucleic acid-assisted generation of targeted double-stranded DNA breaks with T7 endonuclease I
Authors: Aman Rashid , Syed Muntjeeb M , Saleh Ahmed , Melliti Firdaws , Gundra Sivakrishna Rao , Wang Qiaochu , Marsic Tin , Mahas Ahmed , Mahfouz Magdy M
Published: February 2024

Gene-editing technologies have revolutionized biotechnology, but current gene editors suffer from several limitations. Here, we harnessed the power of gamma-modified peptide nucleic acids (γPNAs) to facilitate targeted, specific DNA invasion and used T7 endonuclease I (T7EI) to recognize and cleave the γPNA-invaded DNA. Our data show that T7EI can specifically target PNA-invaded linear and circular DNA to introduce double-strand breaks (DSBs). Our PNA-Guided T7EI (PG-T7EI) technology demonstrates that T7EI can be used as a programmable nuclease capable of generating single or multiple specific DSBs in vitro under a broad range of conditions and could be potentially applied for large-scale genomic manipulation. With no protospacer adjacent motif (PAM) constraints and featuring a compact protein size, our PG-T7EI system will facilitate and expand DNA manipulations both in vitro and in vivo, including cloning, large-fragment DNA assembly, and gene editing, with exciting applications in biotechnology, medicine, agriculture, and synthetic biology.
Characterisation and engineering of a thermophilic RNA ligase from Palaeococcus pacificus
Authors: Rousseau Meghan , Oulavallickal Tifany , Williamson Adele , Arcus Vic , Patrick Wayne M , Hicks Joanna
Published: February 2024

RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in next-generation sequencing of microRNAs. Thermophilic RNA ligases belonging to the RNA ligase 3 family are gaining attention for their use in molecular biology, for example a thermophilic RNA ligase from Methanobacterium thermoautotrophicum is commercially available for the adenylation of nucleic acids. Here we extensively characterise a newly identified RNA ligase from the thermophilic archaeon Palaeococcus pacificus (PpaRnl). PpaRnl exhibited significant substrate adenylation activity but low ligation activity across a range of oligonucleotide substrates. Mutation of Lys92 in motif I to alanine, resulted in an enzyme that lacked adenylation activity, but demonstrated improved ligation activity with pre-adenylated substrates (ATP-independent ligation). Subsequent structural characterisation revealed that in this mutant enzyme Lys238 was found in two alternate positions for coordination of the phosphate tail of ATP. In contrast mutation of Lys238 in motif V to glycine via structure-guided engineering enhanced ATP-dependent ligation activity via an arginine residue compensating for the absence of Lys238. Ligation activity for both mutations was higher than the wild-type, with activity observed across a range of oligonucleotide substrates with varying sequence and secondary structure.
Olivine-Hosted Melt Inclusions Track Progressive Dehydration Reactions in Subducting Slabs Across Volcanic Arcs
Authors: Brahm Raimundo , Coulthard Jr Daniel , Zellmer Georg , Kuritani Takeshi , Sakamoto Naoya , Taniuchi Hajime , Yurimoto Hisayoshi , Nakagawa Mitsuhiro , Sato Eiichi
Published: February 2024

The stability and breakdown of mineral phases in subducting slabs control the cycling of trace elements through subduction zones. Stability of key minerals and the partitioning of trace elements between these minerals and liquid phases of interests have been charted by natural sample analysis and experimental constraints. However, systematic study from arc front to far back arc has rarely shown that the expected geochemical variations of the slab liquid are actually recorded by natural samples. Complexities arise by uncertainties on the nature of the slab component (melts, fluids and supercritical liquids), source heterogeneities and transport processes. Using data from olivine-hosted melt inclusions sampled along and across the NE Japan and southern Kurile arcs, we demonstrate that experimentally and thermodynamically constrained phase stabilities in subducted materials indeed control the trace element signatures as predicted by these models and experiments. The main reactions that can be traced across arc are progressive breakdown of light rare earth element-rich accessory phases (e.g. allanite), enhanced dehydration of the lithospheric mantle (serpentine breakdown) and changes in the nature of the slab component. This work elucidates subduction zone elemental cycling in a well-characterized petrogenetic setting and provides important constraints on the interpretation of trace element ratios in arc magmas in terms of the prograde metamorphic reactions within the subducting slab.
Apatite Chemistry as a Petrogenetic Indicator for Mafic Layered Intrusions
Authors: Kieffer Marie A , Dare Sarah A S , Namur Olivier , Mansur Eduardo T
Published: February 2024

Mafic layered intrusions constitute a natural laboratory to investigate petrogenetic processes using trace element variations in apatite chemistry. Although these intrusions are related to large igneous provinces, there is a wide range of parameters that can affect the chemistry of the primary melt (i.e. composition of the source, pressure, temperature, oxygen fugacity), followed by possible crustal contamination. In this study, we use a comprehensive dataset of analyses of cumulus and intercumulus apatite from a variety of mafic layered intrusions to demonstrate the use of apatite as a powerful petrogenetic indicator. The dataset (determined in this study and compiled from the literature) comprises electron microprobe and LA-ICP-MS analyses, as well as in-situ LA-MC-ICP-MS analyses of Sr isotopes in apatite from well documented layered intrusions (Sept-Iles, Skaergaard, Bushveld, Panzhihua) and the Sudbury Igneous Complex. For the first time, we show that high values of (La/Nd)N, Th, U, Pb, and As in apatite correlate with high (87Sr/86Sr)initial and are related to contamination with continental crust. An elevated (Gd/Yb)N ratio might indicate melting of a mantle source deep enough to retain Yb in garnet. We also confirm that increasingly negative Eu anomaly and decreasing Sr/Y ratio in apatite are indicators of fractional crystallisation of plagioclase, and that high Sr/Y is indicative of early saturation of apatite and/or delayed crystallisation of plagioclase. The reversal to more primitive compositions caused by magma mixing is expressed by higher Sr, V, Mg and Sr/Y ratio, and lower REE + Y, As and Na concentrations in apatite following magma replenishment. Lastly, we show that apatite signature can efficiently distinguish a mafic from a felsic intrusion using its REE and Sr content coupled to its Eu anomaly. It is also possible to further identify the more primitive from the more evolved parts of a mafic layered intrusion, using the Lu, Th, V and volatile (F/Cl) content to distinguish intercumulus from cumulus apatite, respectively. Finally, identifying a mafic magmatic system using detrital apatite in till will prove useful for provenance and mineral exploration studies.
The Crucial Role of Race in Twenty-First Century US Political Realignment
Authors: Barber Michael , Pope Jeremy C
Published: February 2024

Traditional realignment theory has fallen out of fashion among political scientists, yet the popular press talk about political realignments with great regularity. However, in this research note we show that political science should reconsider realignment theory because over the last decade American politics has dramatically realigned—but only for white Americans. Specifically, we demonstrate that income has gone from a highly polarizing factor to one in which there is little to no polarization at all, while at the same time education polarization has increased dramatically to become the prominent demographic cleavage in the white segment of the electorate. However, no such realignment has occurred among Black or Latino voters. These differences across racial groups show how it is essential to consider race in theories of realignment, particularly because of the different experiences across racial groups. Realignment theory is quite viable in the twenty-first century, but the lens of race is the key to seeing the white realignment.
Microbiota enterotoxigenic Bacteroides fragilis-secreted BFT-1 promotes breast cancer cell stemness and chemoresistance through its functional receptor NOD1
Authors: Ma Wei , Zhang Lu , Chen Weilong , Chang Zhaoxia , Tu Juchuanli , Qin Yuanyuan , Yao Yuwen , Dong Mengxue , Ding Jiajun , Li Siqin , Li Fengkai , Deng Qiaodan , Yang Yifei , Feng Tingting , Zhang Fanrong , Shao Xiying , He Xueyan , Zhang Lixing , Hu Guohong , Liu Quentin , Jiang Yi-Zhou , Zhu Shu , Xiao Zhi , Su Dan , Liu Tong , Liu Suling
Published: February 2024

Tumor-resident microbiota in breast cancer promotes cancer initiation and malignant progression. However, targeting microbiota to improve the effects of breast cancer therapy has not been investigated in detail. Here, we evaluated the microbiota composition of breast tumors and found that enterotoxigenic Bacteroides fragilis (ETBF) was highly enriched in the tumors of patients who did not respond to taxane-based neoadjuvant chemotherapy. ETBF, albeit at low biomass, secreted the toxic protein BFT-1 to promote breast cancer cell stemness and chemoresistance. Mechanistic studies showed that BFT-1 directly bound to NOD1 and stabilized NOD1 protein. NOD1 was highly expressed on ALDH+ breast cancer stem cells (BCSCs) and cooperated with GAK to phosphorylate NUMB and promote its lysosomal degradation, thereby activating the NOTCH1-HEY1 signaling pathway to increase BCSCs. NOD1 inhibition and ETBF clearance increase the chemosensitivity of breast cancer by impairing BCSCs.
Overcoming provider barriers to therapeutic drug monitoring of tumour necrosis factor inhibitors for rheumatoid arthritis: a qualitative analysis
Authors: Gavan Sean P , Payne Katherine , Barton Anne
Published: February 2024

Objective

Therapeutic drug monitoring (TDM) of tumour necrosis factor-α inhibitors (TNFi), by measuring drug levels and/or anti-drug antibodies, is being considered by various international bodies to improve patient health outcomes and the value of care for people with rheumatoid arthritis. Rheumatology care providers may perceive barriers to adopting TNFi TDM within their own clinical practice, limiting the potential for patients and health care systems to benefit. This study aimed to explore the barriers perceived by rheumatologists that may reduce their uptake of TNFi TDM for rheumatoid arthritis.

Method

Semi-structured one-to-one telephone interviews were performed with a convenience sample of senior rheumatologists with experience of managing people with rheumatoid arthritis. The interviews explored the rheumatologists’ understanding of TDM and their beliefs about how it can be integrated into their own routine practice. Interviews were audio recorded, transcribed verbatim and anonymized. Transcripts were coded inductively and barriers to using TNFi TDM were identified by thematic framework analysis.

Result

A sample of eleven senior rheumatologists were interviewed. The rheumatologists described five barriers to adopting TNFi TDM in routine practice: (i) observing clinical need; (ii) understanding how testing can improve practice; (iii) insufficient clinical evidence; (iv) insufficient resources to pay for testing; and (v) insufficient capability to deliver testing.

Conclusion

Barriers to adopting TNFi TDM in routine care settings will restrict the ability for patients to benefit from effective monitoring strategies as they begin to emerge. Strategies to overcome these barriers are suggested which will require a coordinated response from stakeholders across health care systems.
Patients’ unmet needs and treatment preferences concerning digital ulcers in systemic sclerosis
Authors: Bandini Giulia , Alunno Alessia , Alcacer-Pitarch Begonya , Ruaro Barbara , Galetti Ilaria , El-Aoufy Khadija , Pinheiro Filipe , Campanaro Giulia , Jade Judith , Di Donato Stefano , Muir Lindsay , Moggi Pignone Alberto , Bellando Randone Silvia , Del Galdo Francesco , McMahan Zsuzsanna H , Matucci-Cerinic Marco , Hughes Michael
Published: February 2024

Objective

Digital ulcers (DUs) significantly impact on quality of life and function in patients with systemic sclerosis (SSc). The aim of our survey was to explore patients’ perspectives and their unmet needs concerning SSc-DUs.

Methods

SSc patients were invited through international patient associations and social media to participate in an online survey.

Results

A total of 358 responses were obtained from 34 countries: US (65.6%), UK (11.5%) and Canada (4.5%). Recurrent DUs were found to be common: >10 DUs (46.1%), 5–10 DUs (21.5%), 1–5 DUs (28.5%), 1 DU (3.9%). Fingertip DUs were most frequent (84.9%), followed by those overlying the IP joints (50.8%). The impact of DUs on patients is considerable, from broad-ranging emotional impacts to impact on activities of daily living, and on personal relationships. Around half of the respondents (51.7%) reported that they received wound/ulcer care, most often provided by non-specialist wound care clinics (63.8%). There was significant variation in local (wound) DU care, in particular regarding the use of debridement and pain management. DU-related education was only provided to one-third of patients. One-quarter of the patients (24.6%) were ‘very satisfied’ or ‘satisfied’ that the provided DU treatment(s) relieved their DU symptoms. Pain, limited hand function, and ulcer duration/chronicity were the main reasons for patients to consider changing DU treatment.

Conclusion

Our data show that there is a large variation in DU treatment between countries. Patient access to specialist wound-care services is limited, and only a small proportion of patients had their DU needs met. Moreover, patient education is often neglected. Evidence-based treatment pathways are urgently needed for DU management.
Follow Father or Mother? Understanding the Monoethnic Identification of Biethnic Children in China
Authors: Mu Zheng , Francis-Tan Andrew
Published: February 2024

In China, children’s ethnicity is often decided by their parents at the time of birth or during childhood; individuals are only allowed to be identified by a single ethnicity. Ethnic identification is therefore a contested issue shaped by the intra-family power structures that determine which parent’s ethnic heritage will be passed down. In this paper, we use China’s 2005 and 2015 inter-census surveys to examine the factors impacting the ethnic identification of children in interethnic families. We find the likelihood that children are identified with their fathers’ ethnicity decreased between 2005 and 2015. Relative to children with a minority mother and a Han father, those with a Han mother and a minority father, and those with parents from different minority groups have higher odds of following their father’s ethnicity. Being a girl, being older, having more educated parents, having urban or migrant status, and living in prefectures with a higher concentration of ethnic minorities all tend to lower the odds of identifying with the father. Moreover, stratified models demonstrate that in families where the father is the only minority parent, Islamic heritage positively predicts boys’ adoption of fathers’ ethnicity, but negatively predicts girls’ adoption. Eligibility for bonus points on the college entrance exam is negatively associated with the odds of following father when the mother is the only minority parent, but the association turns positive when the father is the only minority parent. The results illustrate the nuanced social processes involved in the social construction of ethnic identification.
The effects of genotype-by-environment interactions on body condition score across three winter supplemental feed environments in a composite beef cattle breed in Montana
Authors: Ling Ashley S , Hay El Hamidi
Published: February 2024

Cattle operations in the Northern Great Plains region of the United States face extreme cold weather conditions and require nutritional supplementation over the winter season in order for animals to maintain body condition. In cow–calf operations, body condition scores (BCS) measured at calving and breeding have been shown to be associated with several economically important health and fertility traits, so maintenance of BCS is both an animal welfare and economic concern. A low-to-medium heritability has been found for BCS when measured across various production stages, indicating a large environmental influence but sufficient genetic basis for selection. The present study evaluated BCS measured prior to calving (late winter) and breeding (early summer) under three winter supplementation environments in a multitrait linear mixed model. Traits were discretized by winter supplementation and genetic correlations between environments were considered a reflection of evidence for genotype-by-environment interactions between BCS and diet. Winter supplementation treatments were fed October through April and varied by range access and protein content: 1) feedlot environment with approximately 15% crude protein (CP) corn/silage diet, 2) native rangeland access with 1.8 kg of an 18% CP pellet supplement, and 3) native rangeland access with a self-fed 50% CP and mineral supplement. A total of 2,988 and 2,353 records were collected across multiple parities on 1,010 and 800 individuals for prebreeding and precalving BCS, respectively. Heifers and cows came from a composite beef cattle breed developed and maintained by the USDA Fort Keogh Livestock and Range Research Laboratory near Miles City, Montana. Genetic correlations between treatments 1 and 2, 1 and 3, and 2 and 3 were 0.98, 0.78, and 0.65 and 1.00, 0.98, and 0.99 for precalving and prebreeding BCS, respectively. This provides moderate evidence of genotype-by-environment interactions for precalving BCS under treatment 3 relative to treatments 1 and 2, but no evidence for genotype-by-environment interactions for prebreeding BCS. Treatment 3 differed substantially in CP content relative to treatments 1 and 2, indicating that some animals differ in their ability to maintain BCS up to spring calving across a protein gradient. These results indicate the potential for selection of animals with increased resilience under cold weather conditions and high protein, restricted energy diets to maintain BCS.
Stable water isotopes reveal the onset of bud dormancy in temperate trees, whereas water content is a better proxy for dormancy release
Authors: Walde Manuel G , Wenden Bénédicte , Chuine Isabelle , Gessler Arthur , Saurer Matthias , Vitasse Yann
Published: February 2024

Earlier spring growth onset in temperate forests is a visible effect of global warming that alters global water and carbon cycling. Consequently, it becomes crucial to accurately predict the future spring phenological shifts in vegetation under different climate warming scenarios. However, current phenological models suffer from a lack of physiological insights of tree dormancy and are rarely experimentally validated. Here, we sampled twig cuttings of five deciduous tree species at two climatically different locations (270 and 750 m a.s.l., ~ 2.3 °C difference) throughout the winter of 2019–20. Twig budburst success, thermal time to budburst, bud water content and short-term 2H-labelled water uptake into buds were quantified to link bud dormancy status with vascular water transport efficacy, with the objective of establishing connections between the dormancy status of buds and their effectiveness in vascular water transport. We found large differences in the dormancy status between species throughout the entire investigation period, likely reflecting species-specific environmental requirements to initiate and release dormancy, whereas only small differences in the dormancy status were found between the two studied sites. We found strong 2H-labelled water uptake into buds during leaf senescence, followed by a sharp decrease, which we ascribed to the initiation of endodormancy. However, surprisingly, we did not find a progressive increase in 2H-labelled water uptake into buds as winter advanced. Nonetheless, all examined tree species exhibited a consistent relationship between bud water content and dormancy status. Our results suggest that short-term 2H-labelled water uptake may not be a robust indicator of dormancy release, yet it holds promise as a method for tracking the induction of dormancy in deciduous trees. By contrast, bud water content emerges as a cost-effective and more reliable indicator of dormancy release.
Total-evidence phylogeny of the subfamily Cylapinae and the divergence dates for its subgroupings (Insecta: Heteroptera: Miridae)
Authors: Namyatova Anna A , Tyts Veronica D
Published: February 2024

Representatives of the subfamily Cylapinae (Insecta: Heteroptera: Miridae) mostly inhabit the subtropics and tropics. The group currently comprises five tribes: Bothriomirini, Cylapini, Fulviini, Rhinomirini, and Vanniini. Additionally, the Psallopinae are sometimes included in this subfamily as a tribe. The interrelationships within Cylapinae are unknown, the monophyly is doubtful, and a phylogenetic study focusing on the entire subfamily has never been published. The molecular and fossil data analyses show that Miridae occurred at least in the Jurassic. The divergence dates for Cyalpinae tribes are unknown. We performed the phylogenetic analysis of Cylapinae based on molecular and morphological data, in addition to a combined dataset. We calibrated the molecular trees with fossil data. The results suggested non-monophyly of Cylapinae. The monophyly of Bothriomirini was confirmed. Cylapini were rendered as non-monophyletic. The Cylapus complex formed a clade with Vanniini, and the monophyly of Vanniini was doubtful. Fulviini were recovered as non-monophyletic, and the representatives fell into two separate well-supported clades. Dating analyses showed that the groups of the suprageneric level distributed across different continents diverged near the boarder between Mesosoic and Cenosoic, that was also true for the Asian suprageneric groups and the South American Cylapus complex. Australian groups of genera diverged in the Cenozoic.
Identification and Biological Characterization of a New Cyst Nematode, Heterodera glycines sbsp.n. tabacum, Parasitizing Tobacco in China
Authors: Ren Haohao , Chen Kunyuan , Xu Xiangkui , Li Rongchao , Kang Xiaobo , Chang Fujie , Zhou Yang , Peng Deliang , Zhou Yuan , Jiang Shijun , Cui Jiangkuan
Published: February 2024

In an investigation of diseases from plant-parasitizing nematodes in Henan Province, a cyst nematode was found on tobacco roots and in rhizosphere soil. We identified this strain as a new cyst nematode subspecies, Heterodera glycines sbsp.n. tabacum. The cysts and second-stage juveniles (J2s) parasitizing Henan tobacco were larger than those of H. glycines. A single 345-bp fragment was amplified from H. glycines sbsp.n. tabacum, whereas the 345- and 181-bp fragments were amplified from the soybean cyst nematode. Thus, H. glycines sbsp.n. tabacum was distinct from H. glycines. There were base transversions at 504 sites and base transitions at 560, 858, 920, and 921 sites in the rDNA-ITS sequences of H. glycines sbsp.n. tabacum compared with H. glycines, and there were base transitions at 41, 275, 278, and 380 sites in the mtDNA-COI sequences. In the phylogenetic tree based on the rDNA-ITS and mtDNA-COI regions, H. glycines sbsp.n. tabacum was clustered on a single branch. Based on the randomly amplified polymorphic DNA (RAPD) technique, sequence characterized amplified region (SCAR)-PCR primers were designed. A single 1,113-bp fragment was amplified by specific primers (HtF1/HtR1) from H. glycines sbsp.n. tabacum, while no fragments were obtained from H. glycines. The H. glycines sbsp.n. tabacum can infect soybean plants but cannot complete its life cycle on soybean. Eleven tested tobacco cultivars were infected, with an average reproduction factor (Rf) of 9.74 and a maximum of 64.2 in ‘K326’. The cumulative egg hatching rate of H. glycines sbsp.n. tabacum in the presence of tobacco root exudates was 42.6% at 32 days posthatching, which was significantly greater than that in the presence of soybean root exudates (30.3%) or sterile water (33.1%). In summary, the cyst nematode population parasitizing Henan tobacco was identified as a new subspecies, H. glycines sbsp.n. tabacum.
FilGAP controls cell‐extracellular matrix adhesion and process formation of kidney podocytes
Authors: Saito Koji , Yokawa Seiji , Kurihara Hidetake , Yaoita Eishin , Mizuta Sari , Tada Kanae , Oda Moemi , Hatakeyama Hiroyasu , Ohta Yasutaka
Published: February 2024

The function of kidney podocytes is closely associated with actin cytoskeleton regulated by Rho small GTPases. Loss of actin‐driven cell adhesions and processes is connected to podocyte dysfunction, proteinuria, and kidney diseases. FilGAP, a GTPase‐activating protein for Rho small GTPase Rac1, is abundantly expressed in kidney podocytes, and its gene is linked to diseases in a family with focal segmental glomerulosclerosis. In this study, we have studied the role of FilGAP in podocytes in vitro. Depletion of FilGAP in cultured podocytes induced loss of actin stress fibers and increased Rac1 activity. Conversely, forced expression of FilGAP increased stress fiber formation whereas Rac1 activation significantly reduced its formation. FilGAP localizes at the focal adhesion (FA), an integrin‐based protein complex closely associated with stress fibers, that mediates cell‐extracellular matrix (ECM) adhesion, and FilGAP depletion decreased FA formation and impaired attachment to the ECM. Moreover, in unique podocyte cell cultures capable of inducing the formation of highly organized processes including major processes and foot process‐like projections, FilGAP depletion or Rac1 activation decreased the formation of these processes. The reduction of FAs and process formations in FilGAP‐depleted podocyte cells was rescued by inhibition of Rac1 or P21‐activated kinase 1 (PAK1), a downstream effector of Rac1, and PAK1 activation inhibited their formations. Thus, FilGAP contributes to both cell‐ECM adhesion and process formation of podocytes by suppressing Rac1/PAK1 signaling.
Gallbladder polypoid lesions: Current practices and future prospects
Authors: Wang Kun , Xu Qingpeng , Xia Lu , Sun Jianing , Shen Kanger , Liu Haoran , Xu Linning , Li Rui
Published: February 2024

Gallbladder polypoid lesions (GPLs) refer to any elevated lesion of the mucosal surface of the gallbladder wall, and the prevalence is estimated to be between 0.9% and 12.1%. GPLs include benign polyps and malignant polyps. Benign polyps are further classified as non-neoplastic polyps and neoplastic polyps. Cholesterol polyps are the most common benign polyps and adenocarcinoma is the main type of malignant polyp. Hepatitis B virus infection, liver function abnormalities, dyslipidemia, and obesity are the main risk factors for GPLs. Studies of biological mechanisms have focused on malignant gallbladder polyps, the development of which is regulated by hormone levels in vivo, gut microbiota, inflammation, oxidative stress, Salmonella typhimurium, and related molecules. Diagnostic modalities include chemical examination and imaging examination, with imaging examination currently being the mainstay. Treatment of patients with GPLs is based on the presence or absence of symptoms, age, size of the polyps, tendency of the polyp to increase, and risk factors for symptomatic malignancy to determine whether surgery should be performed.
Histopathological Evaluation of Pouch Neoplasia in Inflammatory Bowel Diseases and Familial Adenomatous Polyposis
Authors: Ko Huaibin Mabel
Published: February 2024

BACKGROUND:

Ileal pouch-anal anastomosis is often required for patients with ulcerative colitis or familial adenomatous polyposis after colectomy. This procedure reduces but does not completely eliminate the risk of neoplasia.

OBJECTIVE:

This study focuses on the histopathology of neoplasia in the ileal pouch, rectal cuff, and anal transition zone.

DATA SOURCES:

We performed a Medline search for English language studies published between 1981 and 2022 using the PubMed search engine. The terms “ileal pouch-anal anastomosis,” “pouchitis,” “pouch dysplasia,” “pouch lymphoma,” “pouch squamous cell carcinoma,” “pouch adenocarcinoma,” “pouch neoplasia,” “dysplasia of rectal cuff,” and “colitis-associated dysplasia” were used.

STUDY SELECTION:

Human studies of neoplasia occurring in the pouch and para-pouch were selected and the full text was reviewed. Comparisons were made within and across studies, with key concepts selected for inclusion in this manuscript.

CONCLUSIONS:

Neoplasia in the pouch is a rare complication in patients with ileal pouch-anal anastomosis. Annual endoscopic surveillance is recommended for familial adenomatous polyposis patients and UC patients with a history of prior dysplasia or carcinoma. In familial adenomatous polyposis, dysplastic polyps of the pouch are visible and readily amenable to endoscopic removal; however, glandular dysplasia in the setting of ulcerative colitis may be invisible on endoscopy. Therefore random biopsies and adequate tissue sampling of the pouch and rectal cuff are recommended in this setting. The histological diagnosis of inflammatory bowel disease-associated dysplasia can be challenging and should be confirmed by at least one expert gastrointestinal pathologist. See video from symposium.
Total Chemical Matricectomy With 88% Phenol: A Prospective Case Series of 37 Patients
Authors: Matter Adriana , Di Chiacchio Nilton Gioia , Iorizzo Matilde , Di Chiacchio Nilton
Published: February 2024

BACKGROUND

Definitive nail dystrophies, congenital, traumatic, or acquired, affecting mainly elderly patients, may not be sufficiently managed with a periodic conservative treatment. A definitive surgical treatment may be considered an alternative method, especially in symptomatic patients.

OBJECTIVE

To evaluate the effectiveness of total matricectomy with 88% phenol solution to treat some nail dystrophies, not otherwise satisfactorily managed.

METHODS

A series of 48 surgeries were performed on 37 patients. Pain evaluation, interference with shoes and gait, recurrences, and patients' satisfaction with procedure were evaluated.

RESULTS

All patients mentioned some pain or impairment in wearing shoes before surgery. Cosmetic results were remarkable, and most of the patients (95.11%) had a dramatic improvement of their discomfort after the procedure. No severe complications occurred during the 12-month follow-up.

LIMITATIONS

Single-center study and the limited number of patients.

CONCLUSION

Total matricectomy with 88% phenol solution is an effective surgical method with low rates of postoperative morbidity and high success rates for treating symptomatic nail dystrophies. The satisfaction with the cosmetic results is high, and this is a safe procedure for patients with associated comorbidities.
Clinical Outcomes and Indications of In-Office Sutureless Dried Gamma Ray-Sterilized Human Amniotic Membrane Transplantation With Bandage Contact Lenses in Various Ocular Surface Disorders
Authors: Jo Kyu Seong , Kim Kook Young , Lee Yong Woo , Han Sang Beom , Choi Chul Young
Published: February 2024

Purpose:

The purpose of this study was to investigate the efficacy and indications of using dried gamma ray-sterilized amniotic membrane (AM) transplantation with bandage contact lenses for the in-office sutureless treatment of various ocular surface diseases.

Methods:

This study retrospectively included 56 eyes of 52 patients with various ocular surface diseases treated with sutureless dehydrated AM-assisted therapeutic contact lenses. The patients were followed up and assessed 1, 2, and 4 weeks after the treatment, and the therapeutic contact lenses were removed after 1 or 2 weeks. The size of the corneal lesion and the degree of pain experienced by each patient before and after the procedure were measured. Corneal re-epithelization rate and clinical aspects related to re-epithelialization were evaluated.

Results:

Complete corneal re-epithelialization of the epithelial defect was observed in 40 eyes. The complete re-epithelialization rates of persistent epithelial defect caused by infectious ulcers, neurotrophic ulcers, ulcers due to burn, toxic keratopathy, previous penetrating keratoplasty or other corneal surgeries, and severe dry eye disease were 69.2%, 80.0%, 77.8%, 100%, 75.0%, and 100%, respectively. Five patients with uncontrolled infectious ulcers, neurotrophic ulcer, bullous keratopathy, and ulcers associated with rheumatic disease did not show significant improvement. Patient pain scores significantly decreased after the procedure.

Conclusions:

Dehydrated AM transplantation with a bandage contact lens is minimally invasive and easily applicable through in-office procedures. This approach is expected to be more actively applied in various ocular surface disorders, not only in severe corneal diseases but also in relatively mild corneal surface diseases.
Retinal arterial and vein occlusion: is surgery ever indicated?
Authors: Kadonosono Kazuaki , Inoue Maiko , Yanagi Yasuo
Published: February 2024

Purpose of review

To highlight the recent progression in surgical treatments for central retinal vein occlusion (CRVO) and central retinal artery occlusion (CRAO).

Recent findings

Anti-VEGF treatment, accepted as a primary treatment for CRVO, is unable to effectively treat all types of the diseases. Regarding CRAO, there are not any accepted therapies available. There have however been recent innovations in surgery, such as utilizing robotics-assisted tools in cannulation procedures for central retinal artery occlusion, or micro-cystotomy for refractory macular edema resulting from ischemic CRVO.

Refractory macular edema due to CRVO can be treated with aspiration of the fluid found inside the large cysts often seen in edema. The success rate of micro-cystotomy has been reported at 78% in eyes with refractory macular edema. Recent studies have shown that cannulation with tissue plasminogen activator (tPA) is effective for eyes with CRAO due to thrombus.

Recent cannulation or micro-cystotomy procedures can be enhanced with the use of robotic tools which allow us to perform this difficult procedure more easily. Newly developed techn

ology, and consequent developments in surgical procedures, will allow us to deal with unmet needs for retinal vessel occlusive diseases.
Concentrations of Fluoxetine Enantiomers Decline During Pregnancy and Increase After Birth
Authors: Wisner Katherine L. , Avram Michael J. , George Alfred L. , Abramova Tatiana V. , Yang Amy , Caritis Steve N. , Costantine Maged M. , Stika Catherine S.
Published: February 2024

Rationale

Few studies of the effect of the dynamic physiologic changes during pregnancy on plasma concentrations of fluoxetine (FLX) have been published.

Objectives

We determined the change in concentration to dose (C/D) ratios of R- and S-FLX and R- and S-norfluoxetine monthly during pregnancy and postpartum, assessed their relationships to cytochrome P450 (CYP) 2D6 and CYP2C9 metabolizer phenotypes, and evaluated the course of their depressive and anxiety symptoms.

Methods

In this observational study, 10 FLX-treated pregnant individuals provided blood samples at steady state every 4 weeks during pregnancy and once postpartum for measurement of plasma FLX and norfluoxetine enantiomer concentrations. Participants were genotyped for variants in CYP2C9 and CYP2D6 using commercial assays with Taqman probes. At each assessment, depressive and anxiety symptoms were quantified.

Results

The C/D ratios of all FLX and norfluoxetine enantiomers, and the active moiety, decreased steadily through pregnancy and rose after birth. In the final trimester, the mean C/D ratio of the active moiety was 24.9% lower compared with the mean nonpregnant, 12-week postpartum C/D ratio. One individual with CYP2D6 ultrarapid metabolizer status was prescribed the highest FLX dose among participants. In these treated individuals, the mean depressive and anxiety symptoms remained in the mild range across the perinatal period.

Conclusions

These data do not support a recommendation for routine plasma concentration monitoring or CYP2D6 pharmacogenetic testing for pregnant people treated with FLX; however, monitoring for symptom relapse is recommended because of declining plasma drug concentrations.
Effect of Coffee and Chocolate Ingestion on Clozapine Dose and on Plasma Clozapine and Norclozapine Concentrations in Clinical Practice
Authors: Flanagan Robert James , Obee Stephen John , Kim Alice Hyun Min , Every-Palmer Susanna
Published: February 2024

Background

Some reports point to dietary caffeine intake as a cause of increased plasma clozapine concentrations in certain patients.

Methods

We compared clozapine dose and plasma clozapine and N-desmethylclozapine (norclozapine) concentrations in male and female smokers and nonsmokers in relation to reported (i) coffee (caffeine) and (ii) chocolate (caffeine and theobromine) intake in samples submitted for clozapine therapeutic drug monitoring, 1993–2017.

Results

There was information on coffee ingestion for 16,558 samples (8833 patients) from males and 5886 samples (3433 patients) from females and on chocolate ingestion for 12,616 samples (7568 patients) from males and 4677 samples (2939 patients) from females. When smoking was considered, there was no discernible effect of either coffee or chocolate ingestion either on the median dose of clozapine or on the median plasma clozapine and norclozapine concentrations in men and in women. However, cigarette smoking was associated with higher coffee and chocolate consumption. Although male nonsmokers who reported drinking 3 or more cups of coffee daily had significantly higher median plasma clozapine and norclozapine concentrations than those who drank less coffee, they were also prescribed a significantly higher clozapine dose. There was no clear effect of coffee ingestion on plasma clozapine and norclozapine in female nonsmokers.

Implications

Inhibition of clozapine metabolism by caffeine at the doses of caffeine normally encountered in those treated with clozapine is unlikely even in male nonsmokers. Measurement of plasma caffeine in an appropriate sample should be considered in any future investigation into a presumed clozapine-caffeine interaction.