bluuebunny/crossref_metadata_2025 huggingface dataset:
Overview of common practices in calf raising facilities
Authors: Machado Vinicius S , Ballou Michael A
Published: January 2022

In this literature review, we overview some of the common management practices associated with calf rearing in specialized operations of the United States. Given the growing importance of dairy-beef calves entering the beef production of the United States, we overview aspects related to housing, nutrition, and health events during the pre- and post-weaning period. Based on data on dairy animals, we hypothesize how early life experiences could impact the feedlot performances of dairy-beef animals. Most of the large calf raising operations, where the majority of dairy-beef animals are raised, are located in the Central Great Plains and West regions of the United States. Approximately 80% of calves are individually housed, but the type of housing (e.g., outside hutch, inside a barn) varies based on location of calf-raising facilities. Milk-replacer is fed in more than 80% of operations, while milk (saleable or nonsaleable) is fed in approximately 30% of calf raising facilities (some operations fed more than one type of liquid diet). In addition to liquid feed, water and calf starter are offered ad libitum to calves. Adequate starter intake at weaning is crucial for feed transition from pre- to post-weaning period, which occurs at approximately 2 months of age. Then, calves are mainly housed in group pens and transition from calf-starter to total mixed ration (TMR). Health challenges such as scours and bovine respiratory disease (BRD) can hinder the performance of calves and are major causes of morbidity and mortality in calf ranches. Transportation at a very young age and comingling with animals from other dairies can increase the risk of diseases. Current research efforts are focusing on determining individual factors such as body weight (BW) at arrival or biomarkers of inflammation and stress that can be predictive of disease morbidity, mortality, and performance of calves. Future research should focus on how to utilize this information to optimize management and to develop targeted preventative strategies to reduce incidence of diseases and mortality and improve performance during the pre-weaned period. Also, more research is needed to understand how colostrum management, housing, and nutrition can impact the adult performance of dairy-beef animals.
DNA Damage and Repair and Epigenetic Modification in the Role of Oxoguanine Glycosylase 1 in Brain Development
Authors: Bhatia Shama , Arslan Eliyas , Rodriguez-Hernandez Luis David , Bonin Robert , Wells Peter G
Published: January 2022

Oxoguanine glycosylase 1 (OGG1) repairs the predominant reactive oxygen species-initiated DNA lesion 8-oxoguanine. Human OGG1 polymorphisms resulting in reduced DNA repair associate with an increased risk for disorders like cancer and diabetes, but the role of OGG1 in brain development is unclear. Herein, we show that Ogg1 knockout mice at 2–3 months of age exhibit enhanced gene- and sex-dependent DNA damage (strand breaks) and decreased epigenetic DNA methylation marks (5-methylcytosine, 5-hydroxymethylcytosine), both of which were associated with increased cerebellar calbindin levels, reduced hippocampal postsynaptic function, altered body weight with age and disorders of brain function reflected in behavioral tests for goal-directed repetitive behavior, anxiety and fear, object recognition and spatial memory, motor coordination and startle response. These results suggest that OGG1 plays an important role in normal brain development, possibly via both its DNA repair activity and its role as an epigenetic modifier, with OGG1 deficiencies potentially contributing to neurodevelopmental disorders.
Diagnostic, predictive and prognostic biomarkers in systemic lupus erythematosus: current insights
Authors: Lindblom Julius , Mohan Chandra , Parodis Ioannis
Published: January 2022

Purpose of review

Biomarkers for diagnosis, monitoring and prognosis still constitute an unmet need for systemic lupus erythematosus (SLE). Focusing on recent findings, this review summarises the current landscape of biomarkers in lupus.

Recent findings

Urine activated leukocyte cell adhesion molecule (ALCAM) exhibited good diagnostic ability in SLE and lupus nephritis (LN) whereas cerebrospinal fluid neutrophil gelatinase-associated lipocalin (NGAL) showed promise in neuropsychiatric SLE. Urine ALCAM, CD163 and vascular cell adhesion molecule 1 (VCAM-1) may be useful in surveillance of LN. Urine monocyte chemoattractant protein 1 was found to predict treatment response in SLE, and urine CD163 and NGAL treatment response in LN. Serum complement component 3 (C3) and urinary VCAM-1 have been reported to portend long-term renal prognosis in LN.

NGAL holds promise as a versatile biomarker in SLE whereas urine ALCAM, CD163 and VCAM-1 displayed good performance as biomarkers in LN. The overall lack of concerted corroboration of leading candidates across multiple cohorts and diverse populations leaves the current biomarker landscape in SLE in an urgent need for further survey and systematic validation.
Evidence for an Inherited Contribution to Sepsis Susceptibility Among a Cohort of U.S. Veterans
Authors: Kempker Jordan A. , Martin Greg S. , Rondina Matthew T. , Cannon-Albright Lisa A.
Published: January 2022

OBJECTIVES:

Analyze a unique clinical and genealogical resource for evidence of familial clustering of sepsis to test for an inherited contribution to sepsis predisposition.

DESIGN:

Observational study.

SETTING:

Veteran’s Health Affairs (VHA) Genealogy/Phenotype resource, a U.S. genealogy database with veterans individually linked to VHA electronic health records.

PATIENTS:

Sepsis was identified using International Classification of Disease, 9th Edition and 10th Edition codes. There were two comparison groups: one composed of the all veterans with linked data and deep genealogy and the other included 1,000 sets of controls, each set randomly sampled from the entire cohort after matching on sex and 10-year birth year range on a 1:1 ratio with cases.

INTERVENTIONS:

None.

MEASUREMENTS AND MAIN RESULTS:

There were 4,666 cases of sepsis from 2001 to 2018, of which 96% were male and 80% greater than or equal to 65 years old. Utilizing the Genealogical Index of Familiality, there was a significant excess of pairwise relatedness among sepsis cases over that in the control sets sampled from VHA population (p = 0.03). The relative risk (RR) of sepsis among identified relatives compared with the larger linked VHA cohort demonstrated an excess of sepsis cases in the first-degree (RR, 1.39; 95% CI, 1.03–1.92; p = 0.05) and second-degree (RR, 1.50; 95% CI, 1.07–2.17; p = 0.04) relatives that were not demonstrated in higher degree relatives. The sepsis cases clustered into 1,876 pedigrees of which 628 had a significant excess of sepsis cases among the descendants (p < 0.05).

CONCLUSIONS:

The data from this cohort of nearly all male U.S. veterans demonstrate evidence for contribution of an inherited predisposition to sepsis and the existence of pedigrees with a significant excess of diagnoses that provide a valuable resource for identification of the predisposition genes and variants responsible. This complements studies on individual genetic variants toward estimating the heritability patterns and clinical relevance of genetic sepsis predisposition.
Is the urinary kidney injury molecule an optimum biomarker for early detection of obstructive nephropathy? An experimental study
Authors: El-Hefnawy Ahmed S , El-Hussiny Mona A , Ibrahim Ahmed M. A , Ali Khadiga M , Atwa Mohammed A , Barakat Nashwa , Alhefnawy Mohamed , Shokeir Ahmed A
Published: January 2022

Objectives

To evaluate the urinary kidney injury molecule-1 (KIM-1) as a predictor for early detection of acute kidney injury in cases with obstructive nephropathy in an animal model and to correlate urinary KIM-1 with the progress of obstructive nephropathy on a histopathological basis.

Materials and methods

Three models of obstruction were induced in 90 male rats: unilateral partial ureteral obstruction with a normal contra-lateral kidney, with nephrectomy of a contralateral kidney (solitary kidney), and bilateral partial ureteral obstruction. Each group was further divided into 2 subgroups; the sham-group (10 rats) and the disease group (20 rats). Serum creatinine, blood urea nitrogen, and urinary KIM-1 were collected on days 0, 7, and 14. Rats were sacrificed on the 7th and 14th day for histopathological examination of the obstructed kidney.

Results

By the end of first week, there was a significant rise of all biomarker levels in all groups when compared with basal levels. Similarly, biomarker levels at the 14th day were significantly higher than those obtained at the 7th day. The urinary KIM-1 level was not detected in the baseline condition. Expression of urinary KIM-1 showed a significant rise in all models ranging from 22 to 85 fold at the 7th day and even higher levels at the 14th day. Histopathological examination confirmed the presence of different forms of tubular injury.

Conclusions

Urinary KIM-1 is significantly elevated in obstructive uropathy. Such an elevation might be advantageous in the early diagnosis and subsequent early intervention of cases with partial ureteral obstruction.
Management of cardiovascular disease in women with premature ovarian insufficiency: critical quality appraisal of clinical guidelines and algorithm development
Authors: Yang Min , Jiang Li , Yao Nan-nan
Published: January 2022

Objectives:

1) To assess the methodological quality of clinical practice guidelines (CPGs) associated with cardiovascular disease (CVD) in women with premature ovarian insufficiency (POI); 2) to formulate an algorithm to foster the implementation of guidelines by clinicians.

Methods:

A systematic search for CPGs in English and Chinese languages published between 2015 and 2020 was conducted. Assessment was conducted by two reviewers respectively via the Appraisal of Guidelines for Research and Evaluation II instrument. The interappraisal agreement was evaluated. Recommendations pertaining to the management of CVD in women with POI were extracted from high-score CPGs and developed into an algorithm, which was refined on the basis of expert feedback.

Results:

A total of 14 CPGs were included. Three CPGs were evaluated as “high quality,” with five “average” and six considered “low quality.” The consistency of agreement between reviewers was considered as substantial agreement to almost perfect agreement (0.72-0.90). The algorithm consisted of three categories: initial evaluation, management, and subsequent monitoring of CVD in POI. Only “management” had recommendations from all three high-quality CPGs.

Conclusions:

The overall methodological quality of most CPGs regarding CVD in women with POI is moderate to poor. A management algorithm with a clear implementation strategy was developed from high-scoring CPGs. Further research is needed to provide evidence-based health care in this field.
Cosmetic dermatology in menopause
Authors: Levin Yakir S.
Published: January 2022

Skin changes that accompany aging lead many to seek treatments that restore a more youthful appearance. Common issues of concern include skin tone, wrinkles, skin thinning, sagging, laxity and decreased elasticity, and hollowing of the face. This work discusses these concerns and their anatomic bases and highlights evidence for a causal role played by menopause-associated hormonal changes where such evidence exists. In addition, treatment options are discussed, with an emphasis on minimally invasive approaches. A variety of modalities are discussed, including botulinum toxins, fillers, multiple types of lasers, radiofrequency devices, focused ultrasound, chemical peels, and thread lifts. These interventions, often in combination, can achieve goals of patients seeking aesthetic rejuvenation.
Coagulopathy following Crotaliπae snakebites in northeast Florida
Authors: Maharaj Satish , Seegobin Karan , Chang Simone
Published: January 2022

Effects of Crotalinae envenomation vary by geographical areas and research into coagulopathy and effects of antivenom are needed to optimize management. This was a single-center retrospective review with testing on presentation and 4 h after; antivenom administration was noted and data analyzed overall and comparing envenomations. One hundred and nineteen snakebites evaluated with 59 identified as Crotalinae and half receiving antivenom. PT/aPTT was elevated in 20% of water moccasin/copperhead and 21% of rattlesnake bites. DIC-like syndrome occurred in 8% water moccasin/copperhead and 6% rattlesnake bites. Antivenom did not seem to correct PT or aPTT at 4 h follow-up in most cases. Thrombotic microangiopathy was not seen. Coagulopathy was prevalent affecting one in five patients in this cohort and does seem to persist at short interval follow-up, even in those receiving antivenom. We support guidelines recommending clinical monitoring and serial coagulation profiles in such cases. Blood Coagul Fibrinolysis 30:000 – 000 Copyright © 2022 Wolters Kluwer Health, Inc. All rights reserved.
Impact of coronavirus disease 2019 epidemics on prevention and care for HIV and other sexually transmitted infections
Authors: de Lazzari Elisa , Martínez-Mimbrero Alejandra , Chivite Iván , González-Cordón Ana , Mosquera Maria M. , Laguno Montserrat , Costa Josep , Bosch Jordi , Blanco Jose L. , Álvarez-Martinez Miriam , Ugarte Ainoa , Inciarte Alexy , de la Mora Lorena , Torres Berta , Martínez-Rebollar Maria , Ambrosioni Juan , Fernaández Emma , Hurtado Juan Carlos , Mallolas Josep , Miró José M. , Marcos María A. , Martínez Esteban
Published: January 2022

Objective:

To assess the impact of coronavirus disease 2019 (COVID-19) epidemics on the prevention and care for HIV and other sexually transmitted infections at a major reference centre providing preventive and clinical services in Catalonia, Spain.

Design:

We retrospectively compared anonymized clinical and laboratory data from March to December 2020 vs. 2019.

Methods:

Monthly clinical data on HIV preexposure and postexposure prophylaxis users and on adults with HIV infection were retrieved from the administrative hospital database. Monthly tests for HIV, hepatitis B and C, Treponema pallidum, Neisseria gonorrhoeae,and Chlamydia trachomatis, and plasma lipids and glucose were recovered from the laboratory database.

Results:

There were less (↓28%, P 
= 0.003) but more advanced (mean CD4+ cells/μl 305 vs. 370, P 
< 0.001) HIV infections and more gonorrhoea (↑39%, P 
< 0.001) and chlamydia (↑37%, P 
< 0.001) infections in 2020 vs. 2019. In people with HIV, rates of HIV RNA less than 50 copies/ml remained stable (11 vs. 11%, P 
= 0.147) despite less scheduled visits (↓25%, P 
< 0.001). However, they had less antiretroviral prescription changes (↓10%, P 
= 0.018), worse plasma lipids [mean total cholesterol 190 vs. 185 mg/dl, P 
< 0.001;mean low-density lipoprotein (LDL) cholesterol 114 vs. 110 mg/dl, P 
< 0.001; mean triglycerides 136 vs. 125 mg/dl, P 
< 0.001; mean high-density lipoprotein (HDL) cholesterol 47 vs. 48 mg/dl, P 
= 006], and an excess of mortality (↑264%, P 
= 0.006) due in great part not only to COVID-19 but also to other causes.

Conclusion:

In our setting, COVID-19 epidemics was associated with an increase in some prevalent sexually transmitted infections, with less but more advanced HIV infections, and with worse nonvirologic healthcare outcomes and higher mortality in people living with HIV.
Age-Associated Gut Dysbiosis, Marked by Loss of Butyrogenic Potential, Correlates With Altered Plasma Tryptophan Metabolites in Older People Living With HIV
Authors: Ghare Smita , Singhal Richa , Bryant Vaughn , Gautam Sabina , Tirumala Chanakya Charan , Srisailam Praneet Kumar , Reyes-Vega Andrea , Ghooray Dushan , McClain Craig J. , Hoffman Kristi , Petrosino Joseph , Bryant Kendall , Govind Varan , Cohen Ronald , Cook Robert L. , Barve Shirish
Published: January 2022

Background:

Imbalance in tryptophan (TRP) metabolism and its neuroactive metabolites, serotonin and kynurenine (KYN), is a known pathogenic mechanism underlying neurocognitive impairment. Gut microbiota plays an important role in TRP metabolism, and the production of these neuroactive molecules affects neurocognitive function. Although both HIV infection and normal aging independently induce gut dysbiosis and influence TRP metabolism, their interactive effects on compositional/functional changes in gut microbiota and consequent alterations in TRP metabolites remain largely undetermined.

Methods:

Older people living with HIV infection (PLWH, aged 50–70 years, n = 22) were enrolled in this cross-sectional pilot study. Metagenomic analysis of fecal microbiome using 16S Ribosomal ribonucleic acid gene sequencing and metabolomics analysis of plasma using mass spectrometry with a reverse-phase iquid chromatography tandem mass spectrometry were performed. Statistical analyses included the univariate linear regression and Spearman correlation analyses.

Results:

Age-associated changes in plasma levels of key neuroactive TRP metabolites, serotonin and KYN, were seen in PLWH. Specifically, we observed age-dependent decreases in serotonin and increases in KYN and KYN-to-TRP ratio, indicative of dysfunctional TRP metabolism. Furthermore, the gut dysbiosis seen in older PLWH is characterized by a reduction of Firmicutes/Bacteroidetes ratio and butyrate-producing microbial families Lachnospiraceae and Lactobacillaceae. Of importance, correspondent with gut dysbiosis, increasing age was significantly associated with decreased plasma butyrate levels, which in turn correlated positively with serotonin and negatively with KYN/TRP ratio.

Conclusions:

Age-dependent gut microbial dysbiosis distinguished by a decrease in butyrogenic potential is a key pathogenic feature associated with the shift in TRP metabolism from serotonin to KYN in older PLWH.
Novel techniques in the treatment of skin and soft tissue infection
Authors: Dryden Matthew
Published: January 2022

Purpose of review

Global antibiotic resistance is compromising the management of soft tissue infection and Acute Bacterial Skin and Skin Structure Infection (ABSSI). This review describes a novel topical treatment Reactive Oxygen (RO) gel which could compliment and in some situations replace systemic antibiotics.

Recent findings

A novel topical treatment RO gel could have an important role in treatment, infection prevention and antimicrobial stewardship. RO is highly antimicrobial against Gram positive and negative bacteria, by slow release of oxygen radicals over a prolonged period of up to 72 h. It prevents and breaks down biofilm and may support healing by cellular signalling. Much clinical investigation remains to be delivered on RO therapy but there seem few disadvantages in its use and early clinical evaluations are extremely promising.

Managing complicated skin and soft tissue infections require more than just antibiotic treatment. Soft tissue infection healing is often compromised by underlying comorbidities and pathology and increasingly the presence of highly antimicrobial-resistant bacteria. This has been highlighted particularly in war and trauma soft tissue infection. The fundamentals of soft tissue infection repair require early surgical drainage and debridement, correction of compromised physiology and treatment of underlying conditions and appropriate antimicrobial treatment. RO therapy could be an important advance.
Correlation analysis of long-term aged soy sauce taste components
and sensory tests
Authors: Jo Young In , Lee Nan-Hee , Choi Ung-Kyu
Published: January 2022

The aim of this study was to predict the taste of long-term aged soy sauce and to
identify the ingredients that affect sensory characteristics. Based on the
correlation analyses of sensory test scores and contents of taste components in
soy sauce after long-term aging, highly significance correlations were detected
between sensory test scores and, in decreasign order, NaCl, arginine, glutamic
acid, leucine, acetic acid, isoleucine, alanine, aspartic acid and tyrosine
contents. Despite significant relationships between the sensory evaluation score
and contents of taste components, it was not possible to predict taste and
quality based on a single component. A multiple regression model based on 22
taste components explained 94% of the variance in the taste of long-term aged
soy sauce. In a stepwise multiple regression analysis performed by sequentially
inputting four highly significant variables (NaCl, glutamic acid, methionine and
oxalic acid), 69.4% of the variance in taste could be explained.
Analysis of A and E vitamer profiles in domestic raw and processed
seafood consumed in Korea
Authors: Park Ye-Eun , Gwak Yu-Jeong , Kim Jeong , Guan YuSen , Hong Won-Ho , Park Su-Jin , Yoon Na-Young , Kim Yeon-Kye , Han Sang Kuk , Chun Jiyeon
Published: January 2022

Simple simultaneous alkaline extraction (saponification) coupled with HPLC was
validated and applied for the analysis of ten vitamers of A (retinol and
β-carotene) and E (α-, β-, γ-, and
δ-tocopherols (T) and corresponding tocotrienols (T3)) in seafood. Limits
of detection for retinol, β-carotene and α-T were 0.380
μg/100 g, 0.602 μg/100 g and 0.0002 mg/100 g, respectively.
Analysis precision was excellent for all vitamers (RSD: repeatability
<2.4%, reproducibility <4.5%). Recoveries of vitamers ranged from
92% to 110%, showing good accuracy. Total vitamin A and E activities varied
among seafood types, with ranges of 0.00-311.77 μg retinol activity
equivalent/100 g and 0.01-0.62 mg α-tocopherol equivalent/100 g,
respectively. β-Carotene was found in some seafoods such as shellfish
(ark shell, blue mussel and spiny top shell) and crustacean (gazami crab)
samples as well as marine algae due to the presence of intestinal organ
containing algae in edible parts. The highest β-carotene content
(689.84±29.86 μg/100 g) was observed in seasoned oyster whereas
the retinol content was highest in blackthroat seaperch (311.77±7.99
μg/100 g). α-T was found in all samples and ranged from 0.07 to
4.72 mg/100 g. This study provides reliable vitamin A and E profiles for
domestic seafood in Korea.
Quality characteristics of sourdough bread produced using banana
sour starter
Authors: Kim Young-Mo
Published: January 2022

This study aimed to investigate the quality characteristics of sourdough produced
using a banana starter. The contents of sugar and alcohol of the banana
fermented broth increased significantly as the fermentation date increased
(p<0.05), and the pH tended to decrease. The titratable acidity of the
fermentation broth increased significantly from the 2nd day of fermentation and
remained high until the 4th day (p<0.05). The pH of dough and bread
decreased as the amount of sour starter added increased (p<0.05), and
there was no significant difference in titratable acidity of dough and bread as
well as the amount of starter. According to the added amount of banana sour, the
moisture content of the bread increased, the crude fat and crude flour content
decreased, and the crude protein content hardly changed. The height of bread
increased in proportion to the increase in the amount of sour starter added. As
for the internal color of the bread, the brightness and yellowness decreased as
the addition amount increased, and the redness increased. It was found that the
volume, specific volume and baking loss rate of bread increased as the amount of
sour starter added increased. In the texture of bread, elasticity and adhesion
increased as the amount added increased, but gumminess, brittleness and hardness
decreased as the amount added increased. From the above results, it is expected
that the banana starter will be used as a useful ingredient in the development
of sourdough bread products.
Characteristics of distillation fractions obtained by various
methods for the distillation of solid-state fermented mash by adding dried
milk
Authors: Shin Je Young , Kang Heui-Yun , Jeong Seok-Tae , Seo Hwa Rang , Kang Chang-Soo , Choi Han-Seok
Published: January 2022

To enhance the flavor of solid-state fermented spirits, the effects of powdered
milk on the composition of the distillation fractions obtained by two different
distillation methods were evaluated. In the solid-state fermented product, the
addition of whole milk powder did not affect alcohol production. However, the
addition of milk increased the amino acid content and reducing sugar content,
and decreased the formic, acetic, and succinic acid contents. Distillation using
a microwave was four times faster than distillation using steam; however, the
resulting number of fractions was high, with a wide range of alcohol flow rates.
After the addition of whole milk powder, the contents of ethyl acetate and ethyl
caproate were 2 times and 16-27 times higher, respectively, in the fraction, and
the contents of butyric, valeric, and hexanoic acids among the volatile organic
acids increased. In addition, the content of furfural, an odor component,
increased 3.45 times from 1,393.73 mg/L to 4,801.93 mg/L. The microwave
distillation method resulted in a 1.46-fold higher ethyl caproate content in the
distillate compared with that obtained by steam distillation. However, as the
temperature of the solid-state fermented mash was raised to over 300°C,
the content of furfural increased by 3.29 times. These results support the use
of milk powder in distilled spirits and may guide the development of optimized
methods.
Cut-and-Paste DNA Insertion with Engineered Type V-K CRISPR-associated Transposases
Authors: Tou Connor J. , Orr Benno , Kleinstiver Benjamin P.
Published: January 2022

CRISPR-associated transposases (CASTs) enable recombination-independent, multi-kilobase DNA insertions at RNA-programmed genomic locations. Type V-K CASTs offer distinct technological advantages over type I CASTs given their smaller coding size, fewer components, and unidirectional insertions. However, the utility of type V-K CASTs is hindered by a replicative transposition mechanism that results in a mixture of desired simple cargo insertions and undesired plasmid co-integrate products. Here, we overcome this limitation by engineering new CASTs with dramatically improved product purity. To do so, we compensate for the absence of the TnsA subunit in multiple type V-K CASTs by engineering a Homing Endonuclease-assisted Large-sequence Integrating CAST compleX, or HELIX system. HELIX utilizes a nicking homing endonuclease (nHE) fused to TnsB to restore the 5 “ nicking capability needed for dual-nicking of the DNA donor. By leveraging distinct features of both type V-K and type I systems, HELIX enables cut-and-paste DNA insertion with up to 99.3% simple insertion product purity, while retaining robust integration efficiencies on genomic targets. Furthermore, we demonstrate the versatility of this approach by generating HELIX systems for other CAST orthologs. We also establish the feasibility of creating a minimal, 3-component HELIX, simplifying the number of proteins that must be expressed. Together, HELIX streamlines and improves the application of CRISPR-based transposition technologies, eliminating barriers for efficient and specific RNA-guided DNA insertions.
Transcriptomic, proteomic and functional consequences of codon usage bias in human cells during heterologous gene expression
Authors: Picard Marion A.L. , Leblay Fiona , Cassan Cécile , Willemsen Anouk , Daron Josquin , Bauffe Frédérique , Decourcelle Mathilde , Demange Antonin , Bravo Ignacio G.
Published: January 2022

Differences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Here, we present a multiscale analysis of the effects of synonymous codon recoding during heterologous gene expression in human cells, quantifying the phenotypic consequences of codon usage bias at different molecular and cellular levels, with an emphasis on translation elongation.

Six synonymous versions of an antibiotic resistance gene were generated, fused to a fluorescent reporter, and independently expressed in HEK293 cells. Multiscale phenotype was analysed by means of: quantitative transcriptome and proteome assessment, as proxies for gene expression; cellular fluorescence, as a proxy for single-cell level expression; and real-time cell proliferation in absence or presence of antibiotic, as a proxy for the cell fitness.

We show that differences in codon usage bias strongly impact the molecular and cellular phenotype: (i) they result in large differences in mRNA levels and in protein levels, leading to differences of over fifteen times in translation efficiency; (ii) they introduce unpredicted splicing events; (iii) they lead to reproducible phenotypic heterogeneity; and (iv) they lead to a trade-off between the benefit of antibiotic resistance and the burden of heterologous expression.

In human cells in culture, codon usage bias modulates gene expression by modifying mRNA availability and suitability for translation, leading to differences in protein levels and eventually eliciting functional phenotypic changes.

IMPORTANCE

Synonymous codons encode for the same amino acid, but they are not neutral regarding gene expression or protein synthesis. Bias between synonymous codons have evolved naturally and are also applied in biotechnology protein production. We have studied the multilevel impact of codon usage on a human cell system. We show that differences in codon usage lead to transcriptomic, proteomic and functional changes, modulating gene expression and cellular phenotype.
PD1+ T-cells correlate with Nerve Fiber Density as a prognostic biomarker in patients with resected perihilar cholangiocarcinoma
Authors: Tan Xiuxiang , Rosin Mika , Appinger Simone , Bednarsch Jan , Liu Dong , Wiltberger Georg , Vallejo Juan Garcia , Lang Sven , Czigany Zoltan , Boroojerdi Shiva , Gaisa Nadine T. , Boor Peter , Bülow Roman David , de Vos-Geelen Judith , Iersel Liselot Valkenburg-van , Groningen Marian Clahsen-van , de Jong Evelien J.M. , Koerkamp Bas Groot , Doukas Michail , Rocha Flavio G. , Luedde Tom , Klinge Uwe , Sivakumar Shivan , Neumann Ulf , Heij Lara
Published: January 2022

Background & Aims

Perihilar cholangiocarcinoma (pCCA) is a rare hepatobiliary malignancy. Nerve fiber invasion (NFI) shows cancer invading the nerve and is considered an aggressive feature. Nerve fiber density (NFD) consists of small nerve fibers without cancer invasion and is divided into high NFD (high numbers of small nerve fibers) or low NFD (low numbers of small nerve fibers). We aim to explore differences in immune cell populations and survival.

Methods

We applied multiplex immunofluorescence (mIF) on 47 pCCA surgically resected patients and investigated the immune cell composition in the tumor microenvironment (TME) of different nerve fiber phenotypes (NFI, high and low NFD). Extensive group comparison was carried out and the association with overall survival (OS) was assessed.

Results

The NFI ROI was measured with highest CD68+ macrophage levels among 3 ROIs (NFI compared to tumor free p= 0.016 and to tumor p=0.034). Further, for NFI patients the density of co-inhibitory markers CD8+PD1+ and CD68+PD1+ were more abundant in the tumor rather than NFI ROI (p= 0.004 and p= 0.0029 respectively). Comparison between patients with NFD and NFI groups, the signals of co-expression of CD8+PD1+ as well as CD68+PD1+ were significantly higher in the high NFD group (p= 0.027 and p= 0.044, respectively). The OS for high NFD patients was 92 months median OS (95% CI:41-142), for low NFD patients 20 months ((95% CI: 4-36) and for NFI group of patients 19 months (95% CI 7-33). The OS for high NFD patients was significantly better compared to low NFD (p= 0.046) and NFI (p= 0.032).

Conclusions

PD1+ T-cells correlate with high NFD as a prognostic biomarker, the biological pathway behind this needs to be investigated.

Lay summary

Nerve fibers play a dual role in the tumor microenvironment in pCCA. In our previous study, we showed that the presence of high numbers of small nerve fibers is associated with a better overall survival. In addition, we found that in high NFD patients PD1+ T-cells are significantly overexpressed. Therefore, we present high NFD as a promising prognostic biomarker.

Graphical abstract
Dynamic Turnover of PI4P and PI(4,5)P2 under Hypoxia Controls Electrostatic Plasma Membrane Targeting
Authors: Lu Juan , Dong Wei , Hammond Gerald R. , Hong Yang
Published: January 2022

Phosphatidylinositol 4-phosphate (PI4P) and phosphatidylinositol 4,5-biphosphate (PIP2) are key phosphoinositides that determine the identity of the plasma membrane (PM) and regulate numerous key biological events there. To date, mechanisms regulating the homeostasis and dynamic turnover of PM PI4P and PIP2 in response to various physiological conditions and stresses remain to be fully elucidated. Here we report that hypoxia in Drosophila induces acute and reversible depletion of PM PI4P and PIP2 that severely disrupts the electrostatic PM targeting of multiple polybasic polarity proteins. Genetically encoded ATP sensors confirmed that hypoxia induces acute and reversible reduction of cellular ATP levels which showed a strong real-time correlation with the levels of PM PI4P and PIP2 in cultured cells. By combining genetic manipulations with quantitative imaging assays we showed that PI4KIIIα, as well as Rbo/EFR3 and TTC7 that are essential for targeting PI4KIIIα to PM, are required for maintaining the homeostasis and dynamic turnover of PM PI4P and PIP2 under normoxia and hypoxia. Our results revealed that in cells challenged by energetic stresses triggered by hypoxia, ATP inhibition and possibly ischemia, dramatic turnover of PM PI4P and PIP2 could have profound impact on many cellular processes including electrostatic PM targeting of numerous polybasic proteins.
Free diffusion of PI(4,5)P2 in the plasma membrane in the presence of high density effector protein complexes
Authors: Pacheco Jonathan , Cassidy Anna C. , Zewe James P. , Wills Rachel C. , Hammond Gerald R. V.
Published: January 2022

The lipid phosphatidyl-D-myo-inositol-4,5-bisphosphate [PI(4,5)P2] is a master regulator of plasma membrane (PM) function. It engages effector proteins that regulate diverse traffic, transport, signaling and cytoskeletal processes that define PM structure and function. How a single class of lipid molecules independently regulate so many parallel processes remains an open question. We tested the hypothesis that spatially segregated pools of PI(4,5)P2 are associated with, and thus reserved for regulation of, different functional complexes in the PM. The mobility of PI(4,5)P2 in the membrane was measured using lipid biosensors by single particle tracking photoactivation localization microscopy (sptPALM). We found that PI(4,5)P2, and several other classes of inner PM lipids, diffuse rapidly at approximately 0.3 µm2/s with largely Brownian motion, although they spend approximately a third of their time diffusing much more slowly. Surprisingly, areas of the PM occupied by PI(4,5)P2-dependent complexes, such endoplasmic-reticulum:PM contact sites, clathrin-coated structures, and several actin cytoskeletal elements including focal adhesions, did not cause a change in PI(4,5)P2 lateral mobility. Only the spectrin and septin cytoskeletons were observed to produce a slowing of PI(4,5)P2 diffusion. We conclude that even structures with high densities of PI(4,5)P2-engaging effector proteins, such as clathrin coated pits and focal adhesions, do not corral free PI(4,5)P2, questioning a role for spatially segregated PI(4,5)P2 pools in organizing and regulating parallel PM functions.
Resource allocation to cell envelopes and the scaling of bacterial growth rate
Authors: Trickovic Bogi , Lynch Michael
Published: January 2022

1

Although various empirical studies have reported a positive correlation between the specific growth rate and cell size across bacteria, it is currently unclear what causes this relationship. We conjecture that such scaling occurs because smaller cells have a larger surface-to-volume ratio and thus have to allocate a greater fraction of the total resources to the production of the cell envelope, leaving fewer resources for other biosynthetic processes. To test this theory, we developed a coarse-grained model of bacterial physiology composed of the proteome that converts nutrients into biomass, with the cell envelope acting as a resource sink. Assuming resources are partitioned to maximize the growth rate, the model yields expected scalings. Namely, the growth rate and ribosomal mass fraction scale negatively, while the mass fraction of envelope-producing enzymes scales positively with surface-to-volume. These relationships are compatible with growth measurements and quantitative proteomics data reported in the literature.
Cancer-driving mutations are enriched in genic regions intolerant to germline variation
Authors: Vitsios Dimitrios , Dhindsa Ryan S. , Mitchell Jonathan , Matelska Dorota , Zou Zoe , Armenia Joshua , Wang Quanli , Sidders Ben , Harper Andrew R. , Petrovski Slavé
Published: January 2022

Large reference datasets of protein-coding variation in human populations have allowed us to determine which genes and genic sub-regions are intolerant to germline genetic variation. There is also a growing number of genes implicated in severe Mendelian diseases that overlap with genes implicated in cancer. Here, we hypothesized that mitotically mutable genic sub-regions that are intolerant to germline variation are enriched for cancer-driving mutations. We introduce a new metric, OncMTR, which uses 125,748 exomes in the gnomAD database to identify genic sub-regions intolerant to germline variation but enriched for hematologic somatic variants. We demonstrate that OncMTR can significantly predict driver mutations implicated in hematologic malignancies. Divergent OncMTR regions were enriched for cancer-relevant protein domains, and overlaying OncMTR scores on protein structures identified functionally important protein residues. Finally, we performed a rare variant, gene-based collapsing analysis on an independent set of 394,694 exomes from the UK Biobank and find that OncMTR dramatically improves genetic signals for hematologic malignancies. Our web app enables easy visualization of OncMTR scores for each protein-coding gene (https://astrazeneca-cgr-publications.github.io/OncMTR-Viewer/).
Isolation and Characterization of Extracellular Vesicles from the Fungal PhytopathogenColletotrichum higginsianum
Authors: Rutter Brian D. , Chu Thi-Thu-Huyen , Zajt Kamil K. , Dallery Jean-Félix , O’Connell Richard J. , Innes Roger W.
Published: January 2022

Fungal phytopathogens secrete extracellular vesicles (EVs) associated with enzymes and phytotoxic metabolites. While these vesicles are thought to promote infection, defining the true contents and functions of fungal EVs, as well as suitable protein markers, is an ongoing process. To expand our understanding of fungal EVs and their possible roles during infection, we purified EVs from the hemibiotrophic phytopathogenColletotrichum higginsianum, the causative agent of anthracnose disease in multiple plant species, includingArabidopsis thaliana. EVs were purified in large numbers from the supernatant of protoplasts but not the supernatant of intact mycelial cultures. We purified two separate populations of EVs, each associated with over 700 detected proteins, including proteins involved in vesicle transport, cell wall biogenesis and the synthesis of secondary metabolites. We selected two SNARE proteins (Snc1 and Sso2) and one 14-3-3 protein (Bmh1) as potential EV markers and generated transgenic lines expressing fluorescent fusions. Each marker was confirmed to be protected inside EVs. Fluorescence microscopy was used to examine the localization of each marker during infection onArabidopsisleaves. These findings further our understanding of EVs in fungal phytopathogens and will help build an experimental system to study EV inter-kingdom communication between plants and fungi.
Retinal axial motion analysis and implications for real-time correction in human retinal imaging
Authors: Cai Yao , Grieve Kate , Mecê Pedro
Published: January 2022

High-resolution ophthalmic imaging devices including spectral-domain and full-field optical coherence tomography (SDOCT and FFOCT) are adversely affected by the presence of continuous involuntary retinal axial motion. Here, we thoroughly quantify and characterize retinal axial motion with both high temporal resolution (200,000 A-scans/s) and high axial resolution (4.5 µm), recorded over a typical data acquisition duration of 3 s with an SDOCT device over 14 subjects. We demonstrate that although breath-holding can help decrease large-and-slow drifts, it increases small-and-fast fluctuations, which is not ideal when motion compensation is desired. Finally, by simulating the action of an axial motion stabilization control loop, we show that a loop rate of 1.2 kHz is ideal to achieve 100% robust clinical in-vivo retinal imaging.
Sex differences in the alcohol-mediated modulation of BLA network states
Authors: DiLeo Alyssa , Antonodiou Pantelis , Ha Spencer , Maguire Jamie L.
Published: January 2022

About 85% of adults in the United States report drinking alcohol in their lifetime. Mood disorders, like generalized anxiety disorder and major depression, are highly comorbid with alcohol use. The basolateral amygdala (BLA) is an area of the brain that is heavily implicated in both mood disorders and alcohol use disorder. Importantly, modulation of BLA network/oscillatory states via parvalbumin-positive (PV) GABAergic interneurons has been shown to control the behavioral expression of fear and anxiety. Further, PV interneurons express a high density of δ-subunit-containing GABAAreceptors (GABAARs), which are sensitive to low concentrations of alcohol. Our lab previously demonstrated that δ-subunit-containing GABAARs on PV interneurons in the BLA influence voluntary ethanol intake and anxiety-like behavior in withdrawal. Therefore, we hypothesized that the effects of alcohol may modulate BLA network states that have been associated with fear and anxiety behaviors via δ-GABAARs on PV interneurons in the BLA. Given the impact of ovarian hormones on the expression of δ-GABAARs, we examined the ability of alcohol to modulate local field potentials (LFPs) in the BLA from male and female C57BL/6J andGabrd-/-mice after acute and repeated exposure to alcohol. Here, we demonstrate that acute and repeated alcohol can differentially modulate oscillatory states in male and female C57BL/6J mice, a process which involves δ-GABAARs. This is the first study to demonstrate that alcohol is capable of altering network states implicated in both anxiety and alcohol use disorders.

Significance Statement

Alcohol use disorder and mood disorders are highly comorbid. The basolateral amygdala (BLA) is implicated in both of these disorders, but the mechanisms contributing to their shared pathophysiology remain uncertain. Here we demonstrate that acute and repeated alcohol exposure can alter network oscillations in the BLA which control the behavioral expression of fear and anxiety. These data suggest that alcohol may directly influence network states associated with mood. Further, we demonstrate sex differences in alcohol’s ability to modulate BLA network states, an effect involving δ-GABAAreceptors, which may contribute to sex differences in alcohol intake and comorbid mood disorders. These data potentially point to a novel mechanism mediating the effects of alcohol on affective states.
Glucocorticoid receptor dysregulation underlies 5-HT2Areceptor-dependent synaptic and behavioral deficits in a mouse neurodevelopmental disorder model
Authors: Saunders Justin M. , Muguruza Carolina , Sierra Salvador , Moreno José L. , Callado Luis F. , Meana J. Javier , Beardsley Patrick M. , González-Maeso Javier
Published: January 2022

Prenatal environmental insults increase the risk of neurodevelopmental psychiatric conditions in the offspring. Structural modifications of dendritic spines are central to brain development and plasticity. Using maternal immune activation (MIA) as a rodent model of prenatal environmental insult, previous results have reported dendritic structural deficits in the frontal cortex. However, very little is known about the molecular mechanism underlying MIA-induced synaptic structural alterations in the offspring. Using prenatal (E12.5) injection with poly-(I:C) as a mouse MIA model, we show that upregulation of the serotonin 5-HT2Areceptor (5-HT2AR) is at least in part responsible for some of the effects of prenatal insults on frontal cortex dendritic spine structure and sensorimotor gating processes. Mechanistically, we report that this upregulation of frontal cortex 5-HT2AR expression is associated with MIA-induced reduction of nuclear translocation of the glucocorticoid receptor (GR) and, consequently, a decrease in the enrichment of GR at the5-HT2ARpromoter. The translational significance of these preclinical findings is supported by data in postmortem human brain samples suggesting dysregulated nuclear GR translocation in frontal cortex of schizophrenia subjects. Repeated (twice a day for 4 days) corticosterone administration augmented frontal cortex5-HT2ARexpression and reduced GR binding to the5-HT2ARpromoter. However, virally (AAV)-mediated augmentation of GR function reduced frontal cortex5-HT2ARexpression and improved sensorimotor gating processes via 5-HT2AR. Together, these data support a negative regulatory relationship between GR signaling and5-HT2ARexpression in mouse frontal cortex that may carry implications for the pathophysiology underlying5-HT2ARdysregulation in neurodevelopmental psychiatric disorders.
Antibiotic action revealed by real-time imaging of the mycobacterial membrane
Authors: Wuo Michael G. , Dulberger Charles L. , Brown Robert A. , Sturm Alexander , Ultee Eveline , Bloom-Ackermann Zohar , Choi Catherine , Garner Ethan C. , Briegel Ariane , Hung Deborah T. , Rubin Eric J. , Kiessling Laura L.
Published: January 2022

The current understanding of mycobacterial cell envelope remodeling in response to antibiotics is limited. Chemical tools that report on phenotypic changes with minimal cell wall perturbation are critical to understanding such time-dependent processes. We employed a fluorogenic chemical probe to image how antibiotics perturb mycobacterial cell envelope assembly in real-time. Time-lapse microscopy revealed that differential antibiotic treatment elicited unique cellular phenotypes, providing a platform for simultaneously monitoring cell envelope construction and remodeling responses. Our data show that rifampicin, which does not directly inhibit cell wall biosynthesis, affords a readily detected mycomembrane phenotype. The fluorogenic probe revealed the production of extracellular vesicles in response to antibiotics, and analyses of these vesicles indicate that antibiotic treatment elicits the release of agents that attenuate macrophage activation.