bluuebunny/crossref_metadata_2025 huggingface dataset:
The Integrity of Retinal Morphology in Non-immunocompromised People Living with HIV on Antiretroviral Therapy
Authors: Munsamy Alvin Jeffrey , Moodley Anandan Angamuthu , Brautaset Rune Lysnes
Published: October 2021

SIGNIFICANCE

Non-immunocompromised people living with HIV (NIPLHIV) share a similar immunocompetence to non-HIV (HIV) people with an elevated cluster of differentiation 4 (CD4) count in the era of antiretroviral therapy (ART). This has reduced the incidence of HIV retinopathy, thus raising the question of the integrity of the retinal morphology in NIPLHIV with longer life expectancy.

PURPOSE

The study assessed the retinal thickness and volume of NIPLHIV without retinitis on ART and attempted to find associations with linear parameters of cerebral atrophy.

METHODS

The study was conducted at a public hospital in South Africa. All people living with HIV were on ART with CD4 counts above 350 cells/mm3 and viral loads less than 10,000 copies/mL. The Heidelberg Spectralis ocular coherence tomographer assessed the retinal thickness and volume for comparison between 30 NIPLHIV and 30 HIV-negative participants. A subset of the HIV group obtained a computed tomography scan to determine the bicaudate ratio and the sylvian fissure ratio to assess cerebral atrophy. Independent t tests were performed to identify differences in retinal thickness and volume. Multivariate linear regressions measured associations between retinal thickness and volume with cerebral atrophy.

RESULTS

The NIPLHIV group had a thicker mean global temporal subfields at Early Treatment Diabetic Retinopathy Study (ETDRS) 3 mm (P = .047) and ETDRS 6 mm (P = .03). The mean global temporal subfield volume at ETDRS 3 mm was also increased in the NIPLHIV group (P = .02). Nasal macula retinal nerve fiber layer thickness and the inferior inner nuclear layer macula volume were directly related to the bicaudate ratio, whereas the volumes at the outer retinal layer subfields of the macula were inversely related to sylvian fissure ratio in NIPLHIV.

CONCLUSIONS

Macula thickness and volumetric differences do exist in NIPLHIV. Practitioners should keep NIPLHIV under retinal morphometric surveillance because they live longer. Associations of cerebral atrophy with retinal morphology may be used to monitor cerebral atrophy in NIPLIV on ART.
Case Report: Retinal Infarction Associated with Migraine
Authors: Slagle William S. , Sheets Savannah R. , Logan Amy B. , Epps Michael , John Vishak J.
Published: October 2021

SIGNIFICANCE

Retinal migraine and migrainous infarction are distinct clinical entities delineated by the International Headache Society. Presented is a novel case report demonstrating unique optical coherence tomography evidence of retinal ischemia experienced during a migraine with effects across retinal vascular territories. This may represent evidence of migrainous infarction within the retina.

PURPOSE

The purpose of this study is to present clinical and quasi-histologic optical coherence tomography features of retinal ischemia associated with migraine.

CASE REPORT

Presented is a case of profound monocular vision loss coincident with a migraine episode. Optical coherence tomography with novel features of acute inner retinal thinning, increased delineation of the inner plexiform and outer plexiform layers, and increased signal intensity of the photoreceptor layer is reported. These discriminating characteristics contrast those of retinal artery occlusions and other primary ocular vasculopathies such as Susac syndrome and acute macular neuroretinopathies.

CONCLUSIONS

A case of permanent vision loss with retinal thinning and ischemic hyperreflectivity of retinal layers on optical coherence tomography in different vascular territories is shown to be associated with migraine. These features may provide clinical evidence of migrainous pathophysiology within the retina.
FDG PET/CT Showing a Primary Vaginal NK/T Cell Lymphoma
Authors: Tang Pan , Wang Rang , Su Minggang , Shen Guohua , Tian Rong
Published: October 2021

A 28-year-old woman with vaginal discharge was admitted to the hospital. Colposcopy examination found several ulcers with pus in the vagina. Biopsy demonstrated extranodal natural killer/T-cell lymphoma. PET/CT scan was subsequently performed for staging. It revealed intense FDG uptake in the vagina. No FDG-avid lesion was seen in the rest of the body. A primary vaginal extranodal natural killer/T-cell lymphoma was diagnosed.
Prognostic Value of FDG PET/CT in Patients With Neuroendocrine Carcinoma of the Uterine Cervix
Authors: Jiang Yuanyuan , Hou Guozhu , Li Fang , Zhu Zhaohui , Cheng Wuying
Published: October 2021

Purpose

We evaluated the prognostic value of metabolic parameters measured on pretreatment FDG PET/CT in patients with cervical neuroendocrine carcinomas (NECs).

Methods

A total of 22 patients with cervical NECs who underwent pretreatment FDG PET/CT were retrospectively reviewed. The SUVmax, metabolic tumor volume (MTV), and total lesion glycolysis (TLG) of the primary lesion were measured. The associations between prognostic factors and progression-free survival (PFS) and overall survival (OS) were investigated using the Kaplan-Meier method, log-rank test, and univariate and multivariate Cox proportional hazards model.

Results

Of the 22 patients, 12 developed disease progression, and 5 died during the follow-up period. Univariate analyses revealed that MTV, TLG, and the International Federation of Gynecology and Obstetrics stage were significantly associated with PFS (all P < 0.05), whereas SUVmax did not show a significant correlation with PFS. Kaplan-Meier survival curves revealed that patients with MTV >31.9 cm3 (log-rank, P < 0.001), TLG >154.3 (log-rank, P < 0.001), and higher International Federation of Gynecology and Obstetrics stage (log-rank, P = 0.026) had significantly shorter PFS. In the multivariate analyses, MTV (P = 0.017; hazard ratio [HR], 7.298; 95% confidence interval [CI], 1.427–37.316) and TLG (P = 0.003; HR, 15.175; 95% CI, 2.470–93.244) were independent prognostic factors, whereas for OS, the univariate analysis revealed that only TLG >154.3 showed statistical significance (P = 0.043; HR, 9.821; 95% CI, 1.080–89.290).

Conclusions

Metabolic tumor volume and TLG on FDG PET/CT were the significant prognostic factors of PFS in patients with cervical NECs. Patients with high MTV and TLG had worse clinical outcomes. In addition, TLG may also be a predictor of OS.
68Ga-FAPI and 18F-PET/CT Images in Intestinal Tuberculosis
Authors: Zheng Jieling , Lin Kaixian , Zheng Shan , Yao Shaobo , Miao Weibing
Published: October 2021

A 28-year-old woman presented with abdominal pain, bowel dysfunction, and weight loss for 3 months. 18F-FDG PET/CT revealed multiple hypermetabolic lesions in the intestines and peritoneal thickening/caking with moderate FDG activity. 68Ga-FAPI PET/CT showed intense FAPI uptake in the aforementioned FDG-avid lesions and a larger number of abnormal foci with intense FAPI uptake in the peritoneum than that shown in 18F-FDG images. Endoscopy-guided biopsy from the colonic mucosa was consistent with tuberculosis. The positive findings of 68Ga-FAPI in the current case highlighted that 68Ga-FAPI may have value in the evaluation of intestinal tuberculosis.
The Superficial Inferior Epigastric Artery Interpolated Flap for Closure of Large Anterolateral Thigh Flap Donor Site Defects
Authors: Jimenez Alejandro Gutierrez , Reategui Alvaro , Lopez Joseph
Published: October 2021

The Anterolateral Thigh (ALT) flap has a critical role in head, neck, and extremity reconstruction. Unfortunately, when the ALT flap is dimensionally large, it leaves an open donor site that may not respond optimally to primary or secondary closure. Traditionally, skin grafting has been used to close large ALT flap donor site defects. However, skin grafting offers less than desirable aesthetic and functional results. The purpose of this article is to present the first reported case of a 70-year-old woman with a large ATL donor site defect, not responsive to direct primary closure, which was successfully reconstructed using a superficial inferior epigastric artery (SIEA) interpolated flap. After 3 weeks, the SIEA interpolated flap was divided, with the patient reporting good outcomes after a 3-month follow-up. The authors suggest that a SIEA interpolated flap as a novel potential approach to optimally repair large ALT donor site defects.
Postoperative Edema Resolution Post-Orthognathic Triple Jaw Surgery: A Three-Dimensional Volumetric Analysis
Authors: Reategui Alvaro , Phillips Sarah , Dinis Jacob , Junn Alexandra , Parsaei Yassmin , Yang Jenny , Lopez Joseph , Steinbacher Derek M.
Published: October 2021

Purpose:

The final result following orthognathic surgery may be hidden for months due to postoperative swelling. However, no substantial evidence supports this time estimate. Our study aims to three-dimensionally quantify volumetric changes in facial edema following triple-jaw surgery.

Materials and Methods:

This was a retrospective, three-dimensional (3D) study of patients who underwent primary orthognathic triple jaw surgery (Le Fort I, Bilateral Sagittal Split Osteotomy (BSSO), and osseous genioplasty) by the senior author (DMS). Vectra 3D Software (Canfield, Fairfield, NJ) was used to assess and quantify volumetric changes between serial 3D photos. An inverse line of best-fit was plotted to assess reduction in postoperative facial edema. The effects of gender, age, body mass index, and tranexamic acid administration on swelling resolution were analyzed through mixed linear model analysis.

Results:

A total of 46 patients (198 images) met the study criteria. The equation for the inverse function line of best fit was y = −13.14ln (x) + 39.54 (P < 0.01). On average, 60% of the swelling resolved in 1 month, 84% after 6 months, and nearly 93% after 12 months. There were no significant differences in the rate of swelling resolution when accounting for age, gender, body mass index, or tranexamic acid administration.

Conclusions:

Most facial edema resolved during the first month following triple jaw surgery, with significant reduction in swelling between 6 and 12 months postoperatively. After 1 year, approximately 10% of the initial edema remained.
Admission Lymphopenia Predicts Infectious Complications and Mortality in Traumatic Brain Injury Victims
Authors: Campbell Brady , Budreau Daniel , Williams-Perez Sophia , Chakravarty Subhashish , Galet Colette , McGonagill Patrick
Published: October 2021

Background:

Traumatic brain injury (TBI) is a major cause of mortality and disability associated with increased risk of secondary infections. Identifying a readily available biomarker may help direct TBI patient care. Herein, we evaluated whether admission lymphopenia could predict outcomes of TBI patients.

Methods:

This is a 10-year retrospective review of TBI patients with a head Abbreviated Injury Score 2 to 6 and absolute lymphocyte counts (ALC) collected within 24 h of admission. Exclusion criteria were death within 24 h of admission and presence of bowel perforation on admission. Demographics, admission data, injury severity score, mechanism of injury, and outcomes were collected. Association between baseline variables and outcomes was analyzed.

Results:

We included 2,570 patients; 946 (36.8%) presented an ALC ≤1,000 on admission (lymphopenic group). Lymphopenic patients were significantly older, less likely to smoke, and more likely to have heart failure, hypertension, or chronic kidney disease. Lymphopenia was associated with increased risks of mortality (OR = 1.903 [1.389–2.608]; P < 0.001) and pneumonia (OR = 1.510 [1.081–2.111]; P = 0.016), increased LOS (OR = 1.337 [1.217–1.469]; P < 0.001), and likelihood of requiring additional healthcare resources at discharge (OR = 1.669 [1.344–2.073], P < 0.001). Additionally, lymphopenia increased the risk of early in-hospital death (OR = 1.459 [1.097–1.941]; P = 0.009). Subgroup analysis showed that lymphopenia was associated with mortality in polytrauma patients and those who presented with two or more concurrent types of TBI. In all subgroup analyses, lymphopenia was associated with longer length of stay and discharge requiring higher level of care.

Conclusion:

A routine complete blood count with differential for all TBI patients may help predict patient outcomes and direct care accordingly.
Penaeicola halotolerans gen. nov., sp. nov., a novel bacterium of the family Cyclobacteriaceae isolated from a shrimp pond
Authors: Ali Sardar , Xie Jianmin , Chen Yuerong , Cai Runlin , Juventus Aweya Jude , Hu Zhong , Zhang Yueling , Wang Hui
Published: October 2021

A Gram-stain-negative, non-motile, rod-shaped, aerobic bacterium (designated as LMIT005T) was isolated from shrimp ponds in Shantou, China. The new isolate was characterized taxonomically using a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain LMIT005T was found to be affiliated with the family

Cyclobacteriaceae

of the order

Cytophagales

while appearing as a distinct lineage. The 16S rRNA gene sequence similarity between strain LMIT005T and

Algoriphagus yeomjeoni

KCTC 12309T, the closest type strain in the family, was 91.3 %. Strain LMIT005T grew optimally at 25 °C, pH 7 and in the presence of 2.0 % (w/v) NaCl. The DNA G+C content (data from genome sequence) was 40.5 mol%. Compared with reference strain

A. yeomjeoni

KCTC 12309T, the average nucleotide identity (ANI) of LMIT005T was 70 %. The sole respiratory quinone of LMIT005T was menaquinone (MK-7), and the major fatty acids were summed feature 3 (C16 : 1 ω6c / C16 : 1 ω7c). The polar lipids of strain LMIT005T were mainly composed of phosphatidylethanolamine, phosphatidylcholine, two unidentified amino lipids, two unidentified lipids, one unidentified glycolipid and one unidentified phospholipid. The draft genome of strain LMIT005T comprised 3 089 781 bp (3.09 Mb) nucleotides and 2773 genes. Antimicrobial resistant-related genes (blal, mexA, and mexb) were annotated in the genome of strain LMIT005T, which indicated that it might be able to resist β-lactam antibiotics. This was further verified by antimicrobial resistant test. Given its distinct genomic, morphological, and physiological differences from previously described type strains, strain LMIT005T is proposed as a representative of a novel genus of the family Cyclobacteriaceae, with the name Penaeicola halotolerans gen. nov., sp. nov. The type strain is LMIT005T (=KCTC 82616T=CICC 25047T).
Head-to-head evaluation of seven different seroassays including direct viral neutralisation in a representative cohort for SARS-CoV-2
Authors: Olbrich Laura , Castelletti Noemi , Schälte Yannik , Garí Mercè , Pütz Peter , Bakuli Abhishek , Pritsch Michael , Kroidl Inge , Saathoff Elmar , Guggenbuehl Noller Jessica Michelle , Fingerle Volker , Le Gleut Ronan , Gilberg Leonard , Brand Isabel , Falk Philine , Markgraf Alisa , Deák Flora , Riess Friedrich , Diefenbach Max , Eser Tabea , Weinauer Franz , Martin Silke , Quenzel Ernst-Markus , Becker Marc , Durner Jürgen , Girl Philipp , Müller Katharina , Radon Katja , Fuchs Christiane , Wölfel Roman , Hasenauer Jan , Hoelscher Michael , Wieser Andreas ,   on behalf of the KoCo19-Study Group
Published: October 2021

A number of seroassays are available for SARS-CoV-2 testing; yet, head-to-head evaluations of different testing principles are limited, especially using raw values rather than categorical data. In addition, identifying correlates of protection is of utmost importance, and comparisons of available testing systems with functional assays, such as direct viral neutralisation, are needed.We analysed 6658 samples consisting of true-positives (n=193), true-negatives (n=1091), and specimens of unknown status (n=5374). For primary testing, we used Euroimmun-Anti-SARS-CoV-2-ELISA-IgA/IgG and Roche-Elecsys-Anti-SARS-CoV-2. Subsequently virus-neutralisation, GeneScriptcPass, VIRAMED-SARS-CoV-2-ViraChip, and Mikrogen-recomLine-SARS-CoV-2-IgG were applied for confirmatory testing. Statistical modelling generated optimised assay cut-off thresholds. Sensitivity of Euroimmun-anti-S1-IgA was 64.8%, specificity 93.3% (manufacturer’s cut-off); for Euroimmun-anti-S1-IgG, sensitivity was 77.2/79.8% (manufacturer’s/optimised cut-offs), specificity 98.0/97.8%; Roche-anti-N sensitivity was 85.5/88.6%, specificity 99.8/99.7%. In true-positives, mean and median Euroimmun-anti-S1-IgA and -IgG titres decreased 30/90 days after RT-PCR-positivity, Roche-anti-N titres decreased significantly later. Virus-neutralisation was 80.6% sensitive, 100.0% specific (≥1:5 dilution). Neutralisation surrogate tests (GeneScriptcPass, Mikrogen-recomLine-RBD) were >94.9% sensitive and >98.1% specific. Optimised cut-offs improved test performances of several tests. Confirmatory testing with virus-neutralisation might be complemented with GeneScriptcPassTM or recomLine-RBD for certain applications. Head-to-head comparisons given here aim to contribute to the refinement of testing strategies for individual and public health use.
Is there an optimal method to detach Candida albicans biofilm from dental materials?
Authors: Moraes Gustavo S. , Cachoeira Victoria S. , Alves Fernanda M. C. , Kiratcz Falyne , Albach Thaís , Bueno Mírian G. , Neppelenbroek Karin H. , Urban Vanessa M.
Published: October 2021

Introduction.
Candida albicans can produce a complex, dynamic and resistant biofilm on the surface of dental materials, especially denture base acrylic resins and temporary soft liners. This biofilm is the main aetiological factor for denture stomatitis, an oral inflammatory condition characterized by chronic and diffuse erythema and oedema of the denture bearing mucosa.

Gap Statement. There is no consensus in the literature regarding the best method to detach biofilms from dental materials. In order to assess the antifungal efficacy of new materials and treatments, the biofilm needs to be properly detached and quantified.

Aim. This study compared different methods of detaching C. albicans biofilm from denture base acrylic resin (Vipi Cril) and temporary soft liner (Softone) specimens.

Methodology. Specimens of each material were immersed in an inoculum of C. albicans SC5314 and remained for 90 min in orbital agitation at 75 r.p.m. and 37 °C. After the removal of non-adherent cells, the specimens were immersed in RPMI-1640 medium for 48 h. Biofilm formation was evaluated with confocal laser scanning microscopy (n=5). Then, other specimens (n=7) were fabricated, contaminated and immersed in 3 ml of sterile phosphate-buffered saline (PBS) and vortexed or sonicated for 1, 2, 5, or 10 min to detach the biofilm. The quantification of detached biofilm was performed by colony-forming unit (c.f.u.) ml−1 count. Results were submitted to one-way analysis of variance (ANOVA)/Tukey HSD test (α=0.05).

Results. A mature and viable biofilm was observed on the surfaces of both materials. For both materials, there was no significant difference (P>0.05) among detachment methods.

Conclusion. Any of the tested methods could be used to detach C. albicans biofilm from hard and soft acrylic materials.
CHD8-associated gastrointestinal complaints are caused by impaired vagal neural crest development and homeostatic imbalance
Authors: Hayot Gaëlle , Massonot Mathieu , Keime Céline , Faure Elodie , Golzio Christelle
Published: October 2021

Gastrointestinal complaints in autism are common and impact the quality of life of affected individuals, yet the underlying mechanisms are understudied. We have found that individuals with mutations inCHD8present with gastrointestinal disturbances. We have shown that loss ofchd8, the sole ortholog ofCHD8in zebrafish, leads to reduced number of enteric neurons and decreased intestinal mobility. However, it remains unclear howchd8acts during the development of the enteric nervous system and whetherCHD8-associated gastrointestinal complaints are solely due to impaired neuronal function in the intestine. Here, utilizing a stablechd8mutant zebrafish model, we found that the loss ofchd8leads to reduced number of vagal neural crest cells (NCCs), enteric neural progenitors, emigrating from the neural tube and their early migration capability was altered. At later stages, although the intestinal colonization by the NCCs was complete, we found decreased numbers of both NCC-derived serotonergic neurons and serotonin-producing enterochromaffin cells, suggesting an intestinal hyposerotonemia in absence ofchd8. Moreover, transcriptomic analyses revealed altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. Next, tissue examination ofchd8mutants revealed thinner intestinal epithelium accompanied by accumulation of neutrophils and decreased numbers of goblet cells and eosinophils. Last, single-cell sequencing of whole mid- and posterior intestines showed a global disruption of the immune balance with perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link betweenchd8, NCC development, intestinal homeostasis, and autism-associated gastrointestinal complaints.
Alphavirus infection triggers selective cytoplasmic translocation of nuclear RBPs with moonlighting antiviral roles
Authors: Kamel Wael , Ruscica Vincenzo , Embarc-Buh Azman , de Laurent Zaydah R. , Garcia-Moreno Manuel , Demyanenko Yana , Madhusudhan Meghana , Iselin Louisa , Järvelin Aino , Hannan Maximilian , Kitano Eduardo , Moore Samantha , Merits Andres , Davis Ilan , Mohammed Shabaz , Castello Alfredo
Published: October 2021

RNA is a central molecule for RNA viruses, acting as mRNA and genome. However, the interactions that viral (v)RNA establishes with the host cell is only starting to be elucidated. Here, we determine with unprecedented depth the composition of the ribonucleoproteins (RNPs) of the prototypical arthropod-borne Sindbis virus (SINV) using viral RNA interactome capture. We show that SINV RNAs engage with hundreds of cellular proteins and pathways, including a group of nuclear RNA-binding proteins (RBPs) with unknown roles in infection. Combining subcellular fractionation and proteomics with several orthogonal approaches, we demonstrate that these nuclear RBPs are selectively redistributed to the cytoplasm after infection, where they associate with the viral replication organelles. These nuclear RBPs potently supress viral gene expression, with activities spanning viral species and families. Our study provides a comprehensive and systematic analysis of SINV RNP composition, revealing a network of nuclear RBPs with moonlighting antiviral function.

Research highlights

SINV RNAs interact with over four hundred cellular RBPs

SINV induces selective cytoplasmic translocation of a subset of nuclear RBPs

These nuclear RBPs display potent antiviral effects

The SF3B complex binds to SINV RNA and supresses infection in a splicing-independent manner
Specific sequence of arrival promotes coexistence via spatial niche preemption by the weak competitor
Authors: Fragata Inês , Costa-Pereira Raul , Kozak Mariya , Majer Agnieszka , Godoy Oscar , Magalhães Sara
Published: October 2021

Historical contingency, such as the order of species arrival, can modify competitive outcomes via niche modification or preemption. However, how these mechanisms ultimately modify stabilising niche and average fitness differences remains largely unknown. By experimentally assembling two congeneric spider mite species feeding on tomato plants during two generations, we show that order of arrival affects species’ competitive ability and changes the outcome of competition. Contrary to expectations, order of arrival did not cause positive frequency dependent priority effects. Instead, coexistence was predicted when the inferior competitor (Tetranychus urticae) arrived first. In that case, T. urticae colonised the preferred feeding stratum (leaves) of T. evansi leading to spatial niche preemption, which equalised fitness and reduced niche differences, driving community assembly to a close-to-neutrality scenario. Our study demonstrates how the order of species arrival and the spatial context of competitive interactions can jointly determine whether species can coexist.
EXOSC10/Rrp6 is essential for the eight-cell embryo/morula transition
Authors: Petit Fabrice G. , Jamin Soazik P. , Kernanec Pierre-Yves , Becker Emmanuelle , Halet Guillaume , Primig Michael
Published: October 2021

The conserved 3’-5’ exoribonuclease EXOSC10/Rrp6 is required for gametogenesis, brain development, erythropoiesis and blood cell enhancer function. The human ortholog is essential for mitosis in cultured cancer cells. Little is known, however, about the role ofExosc10during embryo development and organogenesis. We generated anExosc10knockout model and find thatExosc10−/−mice show an embryonic lethal phenotype. We demonstrate thatExosc10maternal wild type mRNA is present in mutant oocytes and that the gene is expressed during all stages of early embryogenesis. Furthermore, we observe that EXOSC10 early on localizes to the periphery of nucleolus precursor bodies in blastomeres, which is in keeping with the protein’s role in rRNA processing and may indicate a function in the establishment of chromatin domains during initial stages of embryogenesis. Finally, we infer from genotyping data for embryonic days e7.5, e6.5 and e4.5 and embryos culturedin vitrothatExosc10−/−mutants arrest at the eight-cell embryo/morula transition. Our results demonstrate a novel essential role forExosc10during early embryogenesis, and they are consistent with earlier work showing that impaired ribosome biogenesis causes a developmental arrest at the morula stage.
Regulation of drought tolerance in Arabidopsis involves PLATZ4-mediated transcriptional suppression of PIP2;8
Authors: Liu Miao , Wang Chunyan , Ji Zhen , Zhang Lei , Li Chunlong , Huang Jinguang , Yang Guodong , Yan Kang , Zhang Shizhong , Zheng Chengchao , Wu Changai
Published: October 2021

PLATZ transcription factors play important roles in plant growth, development, and biotic and abiotic stress responses. However, how PLATZ regulates plant drought tolerance and ABA sensitivity remains largely unknown. Here, we show that PLATZ4 increases drought tolerance and ABA sensitivity in Arabidopsis thaliana by suppressing the expression of PIP2;8, DEG3, At1g33840 and At3g01345, while upregulating the expression of PR1, ABI3, ABI4 and ABI5. Moreover, PLATZ4 directly binds A/T-rich sequences within the PIP2;8 promoter but not ABI3, ABI4 and ABI5 promoters. Consistent with this, PIP2;8 acts epistatically to PLATZ4. Furthermore, the aquaporin activity of PIP2;8 was confirmed in Xenopus laevis oocytes and yeast cells in response to osmotic stress. Analysis of water loss of seedlings overexpressing PIP2;8 or lacking PIP2;8 function indicated that PIP2;8-mediated water flow is particularly active in response to drought stress in planta. Accordingly, stomatal closure was enhanced in pip2;8 mutants but reduced in PIP2;8-overexpressing plants. In platz4 mutant and PLATZ4-overexpressing plants, water loss and stomatal closure changed oppositely to those in pip2;8 mutants and PIP2;8-overexpressing plants, respectively. In addition, the interaction between PLATZ4 and AITR6 was confirmed by several assays, and the binding of PIP2;8 promoter by PLATZ4 was strengthened by an interaction with AITR6. Collectively, our findings reveal that PLATZ4 interacts with AITR6 to increase ABA sensitivity and drought tolerance in Arabidopsis by upregulating expression of PR1, ABI3, ABI4 and ABI5 while inhibiting the expression of PIP2;8 and associated genes.

One sentence summary

PLATZ4 interacted with AITR6 to increase drought tolerance and ABA sensitivity in Arabidopsis thaliana by directly bind A/T-rich sequences within the plasma membrane aquaporin (PIP)2;8 promoter.
Tuning the sensitivity of genetically encoded fluorescent potassium indicators through structure-guided and genome mining strategies
Authors: Torres Cabán Cristina C. , Yang Minghan , Lai Cuixin , Yang Lina , Subach Fedor , Smith Brian O. , Piatkevich Kiryl D. , Boyden Edward S.
Published: October 2021

Genetically encoded potassium indicators lack optimal binding affinity for monitoring intracellular dynamics in mammalian cells. Through structure-guided design and genome mining of potassium binding proteins, we developed green fluorescent potassium indicators with a broad range of binding affinities. KRaION1, based on the insertion of a potassium binding protein (Ec-Kbp) into the fluorescent protein mNeonGreen, exhibits an isotonically measured Kdof 69±10 (mM; mean ± standard deviation used throughout). We identified Ec-Kbp’s binding site using NMR spectroscopy to detect protein-thallium scalar couplings and refined the structure of Ec-Kbp in its potassium-bound state. Guided by this structure, we modified KRaION1, yielding KRaION2, which exhibits an isotonically measured Kdof 96±9 (mM). We identified four Ec-Kbp homologs as potassium binding proteins, which yielded indicators with isotonically measured binding affinities in the 39-112 (mM) range. KRaIONs expressed and functioned in HeLa cells, but exhibited lower Kdvalues, which were mirrored by lower Kdvalues measured in vitro when holding sodium constant. Thus, potassium indicator Kdmay need to be evaluated in the context of a given experimental goal.
Processive translocation of cohesive and non-cohesive cohesin in vivo
Authors: Borrie Melinda S. , Gartenberg Marc R.
Published: October 2021

Cohesin is a central architectural element of chromosomes that regulates numerous DNA-based events. The complex holds sister chromatids together until anaphase onset and organizes individual chromosomal DNAs into loops. Purified cohesin translocates along DNA in a diffusive fashion that can be propelled by transcribing RNA polymerase. The complex also extrudes DNA loops in a process that consumes ATP. In this study we examine processive genomic translocation of cohesin in vivo. To this end, obstacles of increasing size were tethered to DNA to act as roadblocks to complexes mobilized by transcription in yeast. The obstacles were built from a GFP-lacI core fused to one or more mCherries. A chimera with four mCherries blocked cohesin passage in late G1. During M phase, the threshold barrier depended on the state of cohesion: non-cohesive complexes were also blocked by four mCherries whereas cohesive complexes were blocked by as few as three mCherries. Furthermore, cohesive complexes that were stalled at obstacles, in turn, blocked the passage of non-cohesive complexes. That synthetic barriers alter cohesin redistribution demonstrates that the complex translocates processively on chromatin in vivo. The approach provides a relative measure of the maximum size of the DNA binding chamber(s) of cohesin. Together, this study reveals unexplored limitations to cohesin movement on chromosomes.

Significance Statement

Cohesin is an architectural protein that brings distant chromosomal DNA sites together. The complex links sister chromatids cohesion but it also binds to single pieces of DNA in ways that do not generate cohesion. One class of non-cohesive complexes organizes chromosomal DNA into loops. All cohesin complexes move on DNA but the constraints on such movement are not fully explored. Here, we use size-calibrated obstacles in yeast to interrogate cohesin and the properties of its movement on DNA. We show that both cohesive and non-cohesive complexes translocate processively on chromosomes. In addition, we show that cohesive and non-cohesive complexes are blocked by obstacles of different size. Lastly, we show that stalled cohesive complexes block passage of non-cohesive complexes.
Genomic and metabolic adaptations of biofilms to ecological windows of opportunities in glacier-fed streams
Authors: Busi Susheel Bhanu , Bourquin Massimo , Fodelianakis Stilianos , Michoud Grégoire , Kohler Tyler J. , Peter Hannes , Pramateftaki Paraskevi , Styllas Michail , Tolosano Matteo , De Staercke Vincent , Schön Martina , de Nies Laura , Marasco Ramona , Daffonchio Daniele , Ezzat Leïla , Wilmes Paul , Battin Tom J.
Published: October 2021

Microorganisms dominate life in cryospheric ecosystems. In glacier-fed streams (GFSs), ecological windows of opportunities allow complex microbial biofilms to develop and transiently form the basis of the food web, thereby controlling key ecosystem processes. Here, using high-resolution metagenomics, we unravel strategies that allow biofilms to seize this opportunity in an ecosystem otherwise characterized by harsh environmental conditions. We found a diverse microbiome spanning the entire tree of life and including a rich virome. Various and co-existing energy acquisition pathways point to diverse niches and the simultaneous exploitation of available resources, likely fostering the establishment of complex biofilms in GFSs during windows of opportunity. The wide occurrence of rhodopsins across metagenome-assembled genomes (MAGs), besides chlorophyll, highlights the role of solar energy capture in these biofilms. Concomitantly, internal carbon and nutrient cycling between photoautotrophs and heterotrophs may help overcome constraints imposed by the high oligotrophy in GFSs. MAGs also revealed mechanisms potentially protecting bacteria against low temperatures and high UV-radiation. The selective pressure of the GFS environment is further highlighted by the phylogenomic analysis, differentiating the representatives of the genusPolaromonas, an important component of the GFS microbiome, from those found in other ecosystems. Our findings reveal key genomic underpinnings of adaptive traits that contribute to the success of complex biofilms to exploit environmental opportunities in GFSs, now rapidly changing owing to global warming.
The Relative Binding Position of Nck and Grb2 Adaptors Dramatically Impacts Actin-Based Motility of Vaccinia Virus
Authors: Basant Angika , Way Michael
Published: October 2021

Phosphotyrosine (pTyr) motifs in unstructured polypeptides orchestrate important cellular processes by engaging SH2-containing adaptors to nucleate complex signalling networks. The concept of phase separation has recently changed our appreciation of such multivalent networks, however, the role of pTyr motif positioning in their function remains to be explored. We have now explored this parameter in the assembly and operation of the signalling cascade driving actin-based motility and spread of Vaccinia virus. This network involves two pTyr motifs in the viral protein A36 that recruit the adaptors Nck and Grb2 upstream of N-WASP and Arp2/3-mediated actin polymerization. We generated synthetic networks on Vaccinia by manipulating pTyr motifs in A36 and the unrelated p14 from Orthoreovirus. In contrast to predictions, we find that only specific spatial arrangements of Grb2 and Nck binding sites result in robust N-WASP recruitment, Arp2/3 driven actin polymerization and viral spread. Our results suggest that the relative position of pTyr adaptor binding sites is optimised for signal output. This finding may explain why the relative positions of pTyr motifs are usually conserved in proteins from widely different species. It also has important implications for regulation of physiological networks, including those that undergo phase transitions.
Angiotensin converting enzyme 2 (ACE2) is expressed in murine cutaneous under single-cell transcriptome resolution
Authors: Chu Chenyu , Hu Chen , Liu Li , Wang Yuanjing , Qu Yili , Man Yi
Published: October 2021

Angiotensin converting enzyme 2 (Ace2) is widely distributed in human organs, which was identified as a functional receptor for severe acute respiratory syndrome (SARS) coronavirus in human beings. It was also confirmed that SARS-CoV-2 uses the same cell entry receptor, ACE2, as SARS-CoV. However, related research still not discover the expression data associated with murine skin under single cell RNA resolution. In this study, we performed single-cell RNA sequencing (scRNA-seq) on unsorted cells from mouse dorsal skin after 7 days post-wounding. 8312 sequenced cells from four skin samples met quality control metrics and were analyzed.
The archaeal division protein CdvB1 assembles into polymers that are depolymerized by CdvC
Authors: Jover Alberto Blanch , De Franceschi Nicola , Fenel Daphna , Weissenhorn Winfried , Dekker Cees
Published: October 2021

The Cdv proteins constitute the cell-division system of the Crenarchaea, in a protein machinery that is closely related to the ESCRT system of eukaryotes. The CdvB paralog CdvB1 is believed to play a major role in the constricting ring that is the central actor in cell division in the crenarchaea. Here, we present an in vitro study of purified CdvB1 from the crenarchaeon M. sedula with a combination of TEM imaging and biochemical assays. We show that CdvB1 self-assembles into filamentous polymers that are depolymerized by the action of the Vps4-homolog ATPase CdvC. Using liposome flotation assays, we show that CdvB1 binds to negatively charged lipid membranes and can be detached from the membrane by the action of CdvC. Interestingly, we find that the polymerization and the membrane binding are mutually exclusive properties of the protein. Our findings provide novel insight into one of the main components of the archaeal cell division machinery.
LysM receptors in Coffea arabica: identification, characterization, and gene expression in response to Hemileia vastatrix
Authors: de Lima Santos Mariana , de Resende Mário Lúcio Vilela , dos Santos Ciscon Bárbara Alves , Freitas Natália Chagas , de Brito Pereira Matheus Henrique , Reichel Tharyn , Mathioni Sandra Marisa
Published: October 2021

Pathogen-associated molecular patterns (PAMPs) are recognized by pattern recognition receptors (PRRs) localized on the host plant cell wall. These receptors activate a broad-spectrum and durable defense, which are desired characteristics for disease resistance in plant breeding programs. In this study, candidate sequences for PRRs with lysin motifs (LysM) were investigated in the Coffea arabica genome. For this, approaches based on the principle of sequence similarity, conservation of motifs and domains, phylogenetic analysis, and modulation of gene expression in response to Hemileia vastatrix were used. The candidate sequences for PRRs in C. arabica (Ca1-LYP, Ca2-LYP, Ca1-CERK1, Ca2-CERK1, Ca-LYK4, Ca1-LYK5 and Ca2-LYK5) showed high similarity with the reference PRRs used: Os-CEBiP, At-CERK1, At-LYK4 and At-LYK5. Moreover, the ectodomains of these sequences showed high identity or similarity with the reference sequences, indicating structural and functional conservation. The studied sequences are also phylogenetically related to the reference PRRs described in Arabidopsis, rice, and other plant species. All candidates for receptors had their expression induced after the inoculation with H. vastatrix, since the first time of sampling at 6 hours post-inoculation (hpi). At 24 hpi, there was a significant increase in expression, for most of the receptors evaluated, and at 48 hpi, a suppression. The results showed that the candidate sequences for PRRs in the C. arabica genome display high homology with fungal PRRs already described in the literature. Besides, they respond to pathogen inoculation and seem to be involved in the perception or signaling of fungal chitin, acting as receptors or coreceptors of this molecule. These findings represent an advance in the understanding of the basal immunity of this species.
A Diversity Outbred F1 mouse model identifies host-intrinsic genetic regulators of response to immune checkpoint inhibitors
Authors: Hackett Justin B. , Glassbrook James E. , Muñiz Maria C. , Bross Madeline , Fielder Abigail , Dyson Gregory , Movahhedin Nasrin , McCasland Jennifer , McCarthy-Leo Claire , Gibson Heather M.
Published: October 2021

Immune checkpoint inhibitors (ICI) have improved outcomes for a variety of malignancies; however, many patients fail to benefit. While tumor-intrinsic mechanisms are likely involved in therapy resistance, it is unclear to what extent host genetic background influences response. To investigate this, we utilized the Diversity Outbred (DO) and Collaborative Cross (CC) mouse models. DO mice are an outbred stock generated by crossbreeding 8 inbred founder strains, and CC mice are recombinant inbred mice generated from the same 8 founders. We generated 207 DOB6F1 mice representing 48 DO dams and demonstrated that these mice reliably accept the C57BL/6-syngeneic B16F0 tumor and that host genetic background influences response to ICI. Genetic linkage analysis from 142 mice identified multiple regions including one within chromosome 13 that associated with therapeutic response. We utilized 6 CC strains bearing the positive (NZO) or negative (C57BL/6) driver genotype in this locus. We found that 2/3 of predicted responder CCB6F1 crosses show reproducible ICI response. The chromosome 13 locus contains the murine prolactin family, which is a known immunomodulating cytokine associated with various autoimmune disorders. To directly test whether prolactin influences ICI response rates, we implanted inbred C57BL/6 mice with subcutaneous slow-release prolactin pellets to induce mild hyperprolactinemia. Prolactin augmented ICI response against B16F0, with increased CD8 infiltration and 5/8 mice exhibiting slowed tumor growth relative to controls. This study highlights the role of host genetics in ICI response and supports the use of F1 crosses in the DO and CC mouse populations as powerful cancer immunotherapy models.

One Sentence Summary

Using germline genetic analysis in Diversity Outbred and Collaborative Cross models, we identify prolactin as a host-intrinsic regulator of response to combined immune checkpoint inhibitors.
The DNAPKcs long-range C-NHEJ complex is required for blunt DNA end joining when XLF is weakened
Authors: Cisneros-Aguirre Metztli , Lopezcolorado Felicia Wednesday , Tsai Linda Jillianne , Bhargava Ragini , Stark Jeremy M.
Published: October 2021

Canonical non-homologous end joining (C-NHEJ) factors can assemble into a long-range (LR) complex with DNA ends relatively far apart that contains DNAPKcs, XLF, XRCC4, LIG4, and the KU heterodimer and a short-range (SR) complex lacking DNAPKcs that has the ends positioned for ligation. Since the SR complex can form de novo, the role of the LR complex (i.e., DNAPKcs) for chromosomal EJ is unclear. We have examined EJ of chromosomal blunt DNA double-strand breaks (DSBs), and found that DNAPKcs is significantly less important than XLF and XRCC4 for such EJ. However, weakening XLF via disrupting interaction interfaces (e.g., disrupting the XLF homodimer interface) causes a marked requirement for DNAPKcs, its kinase activity, and its ABCDE-cluster autophosphorylation sites for blunt DSB EJ. In contrast, other aspects of genome maintenance are sensitive to DNAPKcs kinase inhibition in a manner that is not further enhanced by XLF loss (i.e., suppression of homology-directed repair and structural variants, and IR-resistance). We suggest that DNAPKcs is required to position a weakened XLF in an LR complex that can transition into a functional SR complex for blunt DSB EJ, but also has distinct functions for other aspects of genome maintenance.
Dysfunction of cAMP-PKA-calcium signaling axis in striatal medium spiny neurons: a role in schizophrenia and Huntington’s disease pathogenesis
Authors: Fjodorova Marija , Noakes Zoe , De La Fuente Daniel C. , Errington Adam C. , Li Meng
Published: October 2021

Background

Striatal medium spiny neurons (MSNs) are preferentially lost in Huntington’s disease. Genomic studies also implicate a direct role for MSNs in schizophrenia, a psychiatric disorder known to involve cortical neuron dysfunction. It remains unknown whether the two diseases share similar MSN pathogenesis or if neuronal deficits can be attributed to cell type-dependent biological pathways. Transcription factor BCL11B, which is expressed by all MSNs and deep layer cortical neurons, was recently proposed to drive selective neurodegeneration in Huntington’s disease and identified as a candidate risk gene in schizophrenia.

Methods

Using human stem cell-derived neurons lacking BCL11B as a model, we investigated cellular pathology in MSNs and cortical neurons in the context of these disorders. Integrative analyses between differentially expressed transcripts and published GWAS datasets identified cell type-specific disease-related phenotypes.

Results

We uncover a role for BCL11B in calcium homeostasis in both neuronal types, while deficits in mitochondrial function and protein kinase A (PKA)-dependent calcium transients are detected only in MSNs. Moreover, BCL11B-deficient MSNs display abnormal responses to glutamate and fail to integrate dopaminergic and glutamatergic stimulation, a key feature of striatal neurons in vivo. Gene enrichment analysis reveals overrepresentation of disorder risk genes among BCL11B-regulated pathways, primarily relating to cAMP-PKA-calcium signaling axis and synaptic signaling.

Conclusions

Our study indicates that Huntington’s disease and schizophrenia are likely to share neuronal pathogenesis where dysregulation of intracellular calcium levels is found in both striatal and cortical neurons. In contrast, reduction in PKA signaling and abnormal dopamine/glutamate receptor signaling is largely specific to MSNs.
Synthesis and crystal structure of diaquabis(hexamethylenetramine-κN)bis(thiocyanato-κN)cobalt(II)–hexamethylenetetramine–acetonitrile (1/2/2)
Authors: Krebs Christoph , Ceglarska Magdalena , Näther Christian
Published: October 2021

The crystal structure of the title solvated coordination compound, [Co(NCS)2(C6H12N4)2(H2O)2]·2C6H12N4·2C2H3N, consists of discrete complexes in which the Co2+ cations (site symmetry \overline{1}) are sixfold coordinated by two N-bonded thiocyanate anions, two water molecules and two hexamethylenetetramine (HMT) molecules to generate distorted trans-CoN4O2 octahedra. The discrete complexes are each connected by two HMT solvate molecules into chains via strong O—H...N hydrogen bonds. These chains are further linked by additional O—H...N and C—H...N and C—H...S hydrogen bonds into a three-dimensional network. Within this network, channels are formed that propagate along the c-axis direction and in which additional acetonitrile solvent molecules are embedded, which are hydrogen bonded to the network. The CN stretching vibration of the thiocyanate ion occurs at 2062 cm−1, which is in agreement with the presence of N-bonded anionic ligands. XRPD investigations prove the formation of the title compound as the major phase accompanied by a small amount of a second unknown phase.