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Article ; Online: Immunogenicity and efficacy of vaccine boosters against SARS-CoV-2 Omicron subvariant BA.5 in male Syrian hamsters.

Machado, Rafael R G / Walker, Jordyn L / Scharton, Dionna / Rafael, Grace H / Mitchell, Brooke M / Reyna, Rachel A / de Souza, William M / Liu, Jianying / Walker, David H / Plante, Jessica A / Plante, Kenneth S / Weaver, Scott C

Nature communications

2023 Volume 14, Issue 1, Page(s) 4260

Abstract: The SARS-CoV-2 Omicron subvariant BA.5 rapidly spread worldwide and replaced BA.1/BA.2 in many countries, becoming globally dominant. BA.5 has unique amino acid substitutions in the spike protein that both mediate immune escape from neutralizing ... ...

Abstract	The SARS-CoV-2 Omicron subvariant BA.5 rapidly spread worldwide and replaced BA.1/BA.2 in many countries, becoming globally dominant. BA.5 has unique amino acid substitutions in the spike protein that both mediate immune escape from neutralizing antibodies produced by immunizations and increase ACE2 receptor binding affinity. In a comprehensive, long-term (up to 9 months post primary vaccination), experimental vaccination study using male Syrian hamsters, we evaluate neutralizing antibody responses and efficacy against BA.5 challenge after primary vaccination with Ad26.COV2.S (Janssen) or BNT162b2 (Pfizer/BioNTech) followed by a homologous or heterologous booster with mRNA-1273 (Moderna) or NVX-CoV2373 (Novavax). Notably, one high or low dose of Ad26.COV2.S provides more durable immunity than two primary doses of BNT162b2, and the NVX-CoV2373 booster provides the strongest augmentation of immunity, reduction in BA.5 viral replication, and disease. Our data demonstrate the immunogenicity and efficacy of different prime/boost vaccine regimens against BA.5 infection in an immune-competent model and provide new insights regarding COVID-19 vaccine strategies.
MeSH term(s)	Animals ; Cricetinae ; Male ; Humans ; COVID-19 Vaccines ; Ad26COVS1 ; BNT162 Vaccine ; Mesocricetus ; SARS-CoV-2 ; COVID-19/prevention & control ; Vaccines ; Antibodies, Neutralizing ; Antibodies, Viral
Chemical Substances	COVID-19 Vaccines ; Ad26COVS1 (JT2NS6183B) ; BNT162 Vaccine ; Vaccines ; Antibodies, Neutralizing ; Antibodies, Viral
Language	English
Publishing date	2023-07-17
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-023-40033-2
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Article ; Online: The negative impact of shade on photosynthetic efficiency in sugarcane may reflect a metabolic bottleneck

Sales, Cristina R.G. / Ribeiro, Rafael V. / Marchiori, Paulo E.R. / Kromdijk, Johannes / Machado, Eduardo C.

Environmental and Experimental Botany. 2023 July, v. 211 p.105351-

2023

Abstract: Plants with C₄ metabolism normally have higher photosynthetic rates than C₃ ones. As a result, several of the most productive species known are NADP-ME C₄ grasses, such as sugarcane and maize. However, the advantages of the C₄ cycle are most evident ... ...

Abstract	Plants with C₄ metabolism normally have higher photosynthetic rates than C₃ ones. As a result, several of the most productive species known are NADP-ME C₄ grasses, such as sugarcane and maize. However, the advantages of the C₄ cycle are most evident under high light as the CO₂ concentrating mechanism comes at the expense of additional ATP. Recent works have suggested a negative impact of shading across NADP-ME C₄ grasses, causing a downregulation of maximal quantum efficiency of CO₂ assimilation (ϕCO₂,ₘₐₓ). The mechanisms behind the loss in photosynthetic efficiency and whether these results apply for other C₄ crops species and within germplasm of a species remain unclear. We analysed the photosynthetic acclimation to shade in four sugarcane genotypes with contrasting yield. To find out whether the effects of leaf history, i.e., shading a leaf developed under full sunlight and exposed later on to shade differ from a leaf fully developed under shading, these two types of leaves were evaluated. Shaded sugarcane plants showed decreased CO₂ assimilation efficiency compared to plants grown under full sunlight. Based on the fluorescence measurements, it seems that this reduction coincided with a more reduced QA redox state, which could point to a metabolic limitation downstream of the light-dependent reactions. The results were similar for all genotypes and were observed regardless of whether leaves developed under shade or under full sunlight conditions and exposed subsequently to shade, suggesting that light is the main factor affecting photosynthetic efficiency. This study reinforces the notion that this negative impact of shade could reflect a common bottleneck across NADP-ME C₄ grasses.
Keywords	acclimation ; carbon dioxide ; corn ; fluorescence ; germplasm ; leaves ; photosynthesis ; solar radiation ; sugarcane ; ACO2 ; A'CO2 ; Aoperating ; Apotential ; Asat ; CCM ; ci ; CO2_r ; DAP ; Fq'/Fm' ; Fq'/Fv' ; Fv'/Fm' ; gs ; LCP ; Ls ; Q ; Rd ; VPDleaf ; Vmax ; Vp,max, ; θ ; ϕCO2 ; ϕCO2,max ; C4 photosynthesis ; Plasticity ; Photoacclimation ; Photosynthetic light-use efficiency ; Quantum yield, Saccharum spp
Language	English
Dates of publication	2023-07
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	Use and reproduction
ZDB-ID	195968-2
ISSN	0098-8472
ISSN	0098-8472
DOI	10.1016/j.envexpbot.2023.105351
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Article ; Online: Neutralization against Omicron SARS-CoV-2 from previous non-Omicron infection

Jing Zou / Hongjie Xia / Xuping Xie / Chaitanya Kurhade / Rafael R. G. Machado / Scott C. Weaver / Ping Ren / Pei-Yong Shi

Nature Communications, Vol 13, Iss 1, Pp 1-

2022 Volume 4

Abstract: The SARS-CoV-2 variant of concern Omicron has quickly spread. Here, Zou et al. develop a high-throughput neutralization test for Omicron SARS-CoV-2 and show that patients with previous non-Omicron infections do not develop robust neutralization against ... ...

Abstract	The SARS-CoV-2 variant of concern Omicron has quickly spread. Here, Zou et al. develop a high-throughput neutralization test for Omicron SARS-CoV-2 and show that patients with previous non-Omicron infections do not develop robust neutralization against Omicron.
Keywords	Science ; Q
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Assessment of heat production and methane emission using infrared thermography in lactating Holstein and Gyrolando-F1 (½ Holstein ½ Gyr) crossbreed cows.

Guadagnin, Anne R / Matiello, João P / Ribeiro, Rafael S / Pereira, Luiz G R / Machado, Fernanda S / Tomich, Thierry R / Campos, Mariana M / Heisler, Guilherme / Fischer, Vivian

Journal of thermal biology

2023 Volume 115, Page(s) 103628

Abstract: ... feeding in Gyrolando-F1 cows (r = 0.85, P < 0.05) and with IRT taken at the eye 5 h after feeding ... in Holstein cows (r = 0.88, P < 0.05). HP was positively correlated with IRT taken at the eye 6 h after ... feeding in Gyrolando-F1 cows (r = 0.85, P < 0.05) and with IRT taken at the eye 5 h after feeding ...

Abstract	Infrared thermography (IRT) is a non-invasive and efficient tool to detect changes in the animal's body surface temperature, which is directly associated with the animal's energy loss. Methane emission represents a significant energy loss, particularly in ruminants, as well as heat production. Therefore, the aim of this study was to correlate skin temperature measured using IRT with heat production (HP) and methane emission in lactating Holstein and crossbred ½ Holstein x ½ Gyr (Gyrolando-F1) cows. Six Gyrolando-F1 and four Holstein cows, all primiparous, at mid lactation were used to evaluate daily HP and methane emission using indirect calorimetry in respiratory chambers. Thermographic images were taken at anus, vulva, ribs (on the right side), left flank, right flank, right front foot, upper lip, masseter and eye; IRT was performed every hour during 8 h after the morning feeding. Cows received the same diet ad libitum. Daily methane emission was positively correlated with IRT taken at the right front foot 1 h after feeding in Gyrolando-F1 cows (r = 0.85, P < 0.05) and with IRT taken at the eye 5 h after feeding in Holstein cows (r = 0.88, P < 0.05). HP was positively correlated with IRT taken at the eye 6 h after feeding in Gyrolando-F1 cows (r = 0.85, P < 0.05) and with IRT taken at the eye 5 h after feeding in Holstein cows (r = 0.90, P < 0.05). Infrared thermography was positively correlated with HP and methane emission in both Holstein and Gyrolando-F1 lactating cows, although the anatomical points and times of image acquisition yielding the greatest correlation coefficients varies among breeds.
MeSH term(s)	Female ; Cattle ; Animals ; Lactation ; Milk/chemistry ; Methane/analysis ; Thermography ; Diet/veterinary
Chemical Substances	Methane (OP0UW79H66)
Language	English
Publishing date	2023-06-21
Publishing country	England
Document type	Journal Article
ZDB-ID	1498364-3
ISSN	1879-0992 ; 0306-4565
ISSN (online)	1879-0992
ISSN	0306-4565
DOI	10.1016/j.jtherbio.2023.103628
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Article ; Online: Allosteric Inhibition of

Read, Benjamin J / Fisher, Gemma / Wissett, Oliver L R / Machado, Teresa F G / Nicholson, John / Mitchell, John B O / da Silva, Rafael G

ACS infectious diseases

2021 Volume 8, Issue 1, Page(s) 197–209

Abstract: ATP phosphoribosyltransferase (ATPPRT) catalyzes the first step of histidine biosynthesis in bacteria, namely, the condensation of ATP and 5-phospho-α-d-ribosyl-1-pyrophosphate (PRPP) to ... ...

Abstract	ATP phosphoribosyltransferase (ATPPRT) catalyzes the first step of histidine biosynthesis in bacteria, namely, the condensation of ATP and 5-phospho-α-d-ribosyl-1-pyrophosphate (PRPP) to generate
MeSH term(s)	ATP Phosphoribosyltransferase/genetics ; ATP Phosphoribosyltransferase/metabolism ; Acinetobacter baumannii/metabolism ; Dipeptides ; Histidine ; Kinetics
Chemical Substances	Dipeptides ; Histidine (4QD397987E) ; ATP Phosphoribosyltransferase (EC 2.4.2.17)
Language	English
Publishing date	2021-12-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2373-8227
ISSN (online)	2373-8227
DOI	10.1021/acsinfecdis.1c00539
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Article ; Online: Assessment of heat production and methane emission using infrared thermography in lactating Holstein and Gyrolando-F1 (½ Holstein ½ Gyr) crossbreed cows

Guadagnin, Anne R. / Matiello, João P. / Ribeiro, Rafael S. / Pereira, Luiz G.R. / Machado, Fernanda S. / Tomich, Thierry R. / Campos, Mariana M. / Heisler, Guilherme / Fischer, Vivian

Journal of Thermal Biology. 2023 July, v. 115 p.103628-

2023

Abstract	Infrared thermography (IRT) is a non-invasive and efficient tool to detect changes in the animal's body surface temperature, which is directly associated with the animal's energy loss. Methane emission represents a significant energy loss, particularly in ruminants, as well as heat production. Therefore, the aim of this study was to correlate skin temperature measured using IRT with heat production (HP) and methane emission in lactating Holstein and crossbred ½ Holstein x ½ Gyr (Gyrolando-F1) cows. Six Gyrolando-F1 and four Holstein cows, all primiparous, at mid lactation were used to evaluate daily HP and methane emission using indirect calorimetry in respiratory chambers. Thermographic images were taken at anus, vulva, ribs (on the right side), left flank, right flank, right front foot, upper lip, masseter and eye; IRT was performed every hour during 8 h after the morning feeding. Cows received the same diet ad libitum. Daily methane emission was positively correlated with IRT taken at the right front foot 1 h after feeding in Gyrolando-F1 cows (r = 0.85, P < 0.05) and with IRT taken at the eye 5 h after feeding in Holstein cows (r = 0.88, P < 0.05). HP was positively correlated with IRT taken at the eye 6 h after feeding in Gyrolando-F1 cows (r = 0.85, P < 0.05) and with IRT taken at the eye 5 h after feeding in Holstein cows (r = 0.90, P < 0.05). Infrared thermography was positively correlated with HP and methane emission in both Holstein and Gyrolando-F1 lactating cows, although the anatomical points and times of image acquisition yielding the greatest correlation coefficients varies among breeds.
Keywords	Biological Sciences ; Holstein ; animals ; anus ; calorimetry ; crossbreds ; diet ; energy ; eyes ; feet ; heat production ; lactation ; methane production ; skin temperature ; surface temperature ; thermography ; vulva ; Bioenergetics ; Dairy cows ; Greenhouse gases ; Precision technology
Language	English
Dates of publication	2023-07
Publishing place	Elsevier Ltd
Document type	Article ; Online
ZDB-ID	1498364-3
ISSN	1879-0992 ; 0306-4565
ISSN (online)	1879-0992
ISSN	0306-4565
DOI	10.1016/j.jtherbio.2023.103628
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Article ; Online: Neutralization against Omicron SARS-CoV-2 from previous non-Omicron infection.

Zou, Jing / Xia, Hongjie / Xie, Xuping / Kurhade, Chaitanya / Machado, Rafael R G / Weaver, Scott C / Ren, Ping / Shi, Pei-Yong

Nature communications

2022 Volume 13, Issue 1, Page(s) 852

Abstract: The spread of the Omicron SARS-CoV-2 variant underscores the importance of analyzing the cross-protection from previous non-Omicron infection. We have developed a high-throughput neutralization assay for Omicron SARS-CoV-2 by engineering the Omicron ... ...

Abstract	The spread of the Omicron SARS-CoV-2 variant underscores the importance of analyzing the cross-protection from previous non-Omicron infection. We have developed a high-throughput neutralization assay for Omicron SARS-CoV-2 by engineering the Omicron spike gene into an mNeonGreen USA-WA1/2020 SARS-CoV-2 (isolated in January 2020). Using this assay, we determine the neutralization titers (defined as the maximal serum dilution that inhibited 50% of infectious virus) of patient sera collected at 1- or 6-months after infection with non-Omicron SARS-CoV-2. From 1- to 6-month post-infection, the neutralization titers against USA-WA1/2020 decrease from 601 to 142 (a 4.2-fold reduction), while the neutralization titers against Omicron-spike SARS-CoV-2 remain low at 38 and 32, respectively. Thus, at 1- and 6-months after non-Omicron SARS-CoV-2 infection, the neutralization titers against Omicron are 15.8- and 4.4-fold lower than those against USA-WA1/2020, respectively. The low cross-neutralization against Omicron from previous non-Omicron infection supports vaccination of formerly infected individuals to mitigate the health impact of the ongoing Omicron surge.
MeSH term(s)	Antibodies, Neutralizing/immunology ; Antibodies, Viral/immunology ; COVID-19/blood ; COVID-19/immunology ; COVID-19/virology ; Cross Reactions ; Humans ; Neutralization Tests ; Reinfection/blood ; Reinfection/immunology ; Reinfection/virology ; SARS-CoV-2/genetics ; SARS-CoV-2/immunology
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral
Language	English
Publishing date	2022-02-09
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-28544-w
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Article ; Online: A Comparison of Seegene Technologies Novaplex SARS-CoV-2 Variants I, II, and IV Assays with Spike Gene Sequencing for Detection of Known Severe Acute Respiratory Syndrome Coronavirus 2 Variants.

Nielsen, Marisa C / Machado, Rafael R G / Mitchell, Brooke M / McConnell, Allan J / Saada, Nehad I / Weaver, Scott C / Ren, Ping

The Journal of molecular diagnostics : JMD

2022 Volume 24, Issue 5, Page(s) 455–461

Abstract: Tracking new and emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has become increasingly important for public health responses, primarily because of variant-dependent transmission, disease severity, and treatment decisions. ...

Abstract	Tracking new and emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has become increasingly important for public health responses, primarily because of variant-dependent transmission, disease severity, and treatment decisions. This evaluation compared Seegene Technologies Novaplex SARS-CoV-2 Variants I, II, and IV (I,II&IV) assays to detect known SARS-CoV-2 variants using traditional spike gene Sanger sequencing results as the gold standard reference. Both RNA extraction and extraction-free protocols were assessed. A total of 156 samples were included in this study. There was 100% (109/109) overall agreement (95% CI, 96.7%-100%) between the spike gene sequencing and the I,II&IV results using extracted RNA for the variants included in the Novaplex assay menus. The RNA extraction-free method was 91.7% (143/156) as sensitive (95% CI, 86.2%-95.5%) as the traditional RNA extraction method. Using the extraction-free method on samples with higher cycle threshold values (>30) resulted in some mutations not being detected, presumably due to lower nucleic acid concentrations in the original samples. In conclusion, the I,II&IV assays provide an accurate, rapid, and less labor-intensive method for detecting SARS-CoV-2 and identifying known variants of interest and concern. The RNA extraction-free method for samples with cycle threshold of <30 could be cost-effective for surveillance purposes. However, spike gene sequencing retains the advantage of detecting more and new variants.
MeSH term(s)	COVID-19/diagnosis ; Humans ; Mutation ; RNA ; SARS-CoV-2/genetics
Chemical Substances	RNA (63231-63-0)
Language	English
Publishing date	2022-02-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2000060-1
ISSN	1943-7811 ; 1525-1578
ISSN (online)	1943-7811
ISSN	1525-1578
DOI	10.1016/j.jmoldx.2022.02.001
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Article ; Online: Safety and efficacy of teplizumab in the treatment of type 1 diabetes mellitus: An updated systematic review and meta-analysis of randomized controlled trials.

Grando Alves, Gabriel / Cunha, Luisa / Henkes Machado, Rafael / Lins de Menezes, Vanessa

Diabetes, obesity & metabolism

2024

Abstract: Aim: To provide updated efficacy and safety information for teplizumab in the treatment of Stage 3 type 1 diabetes mellitus (T1DM).: Materials and methods: The PubMed, Embase and Cochrane databases were searched for randomized controlled trials (RCTs) ...

Abstract	Aim: To provide updated efficacy and safety information for teplizumab in the treatment of Stage 3 type 1 diabetes mellitus (T1DM). Materials and methods: The PubMed, Embase and Cochrane databases were searched for randomized controlled trials (RCTs) comparing teplizumab to placebo for T1DM that reported any of the following outcomes: (1) C-peptide area under the curve (AUC); (2) glycated haemoglobin (HbA1c) levels; (3) insulin requirements; and (4) adverse events. Heterogeneity was examined with I Results: Eight RCTs with 1052 patients (754 receiving teplizumab) were included. Teplizumab significantly increased the AUC of C-peptide levels at 6 (MD 0.10 nmol/L, 95% CI 0.05, 0.16), 12 (MD 0.13 nmol/L, 95% CI 0.06, 0.20), 18 (MD 0.18 nmol/L, 95% CI 0.09, 0.27) and 24 months (MD 0.16 nmol/L, 95% CI 0.02, 0.31), significantly reduced HbA1c levels at 6 (MD -0.57%, 95% CI -1.07, -0.08) and 12 months (MD -0.31%, 95% CI -0.59, -0.02), and significantly reduced insulin requirements at 6 (MD -0.12 U/kg, 95% CI -0.16, -0.08), 12 (MD -0.11 U/kg, 95% CI -0.15, -0.07), 18 (MD -0.17 U/kg, 95% CI -0.26, -0.09) and 24 months (MD -0.11 U/kg, 95% CI -0.22, -0.01). Conclusion: Teplizumab increases AUC of C-peptide levels and decreases HbA1c levels and insulin use, without raising serious adverse event risk.
Language	English
Publishing date	2024-04-11
Publishing country	England
Document type	Journal Article
ZDB-ID	1454944-x
ISSN	1463-1326 ; 1462-8902
ISSN (online)	1463-1326
ISSN	1462-8902
DOI	10.1111/dom.15581
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Article ; Online: Primary and Secondary Attack Rates by Vaccination Status after a SARS-CoV-2 B.1.617.2 (Delta) Variant Outbreak at a Youth Summer Camp-Texas, June 2021.

Baker, Julia M / Shah, Melisa M / O'Hegarty, Michelle / Pomeroy, Mary / Keiser, Philip / Ren, Ping / Weaver, Scott C / Maknojia, Sara / Machado, Rafael R G / Mitchell, Brooke M / McConnell, Allan / Tate, Jacqueline E / Kirking, Hannah L

Journal of the Pediatric Infectious Diseases Society

2023 Volume 11, Issue 12, Page(s) 550–556

Abstract: Children are capable of initiating COVID-19 transmission into households, but many questions remain about the impact of vaccination on transmission. Data from a COVID-19 Delta variant outbreak at an overnight camp in Texas during June 23-27, 2021, were ... ...

Abstract	Children are capable of initiating COVID-19 transmission into households, but many questions remain about the impact of vaccination on transmission. Data from a COVID-19 Delta variant outbreak at an overnight camp in Texas during June 23-27, 2021, were analyzed. The camp had 451 attendees, including 364 youths aged < 18 years and 87 adults. Detailed interviews were conducted with 92 (20.4%) of consenting attendees and 117 household members of interviewed attendees with COVID-19. Among 450 attendees with known case status, the attack rate was 41%, including 42% among youths; attack rates were lower among vaccinated (13%) than among unvaccinated youths (48%). The secondary attack rate was 51% among 115 household contacts of 55 interviewed index patients. Secondary infections occurred in 67% of unvaccinated household members and 33% of fully or partially vaccinated household members. Analyses suggested that household member vaccination and camp attendee masking at home protected against household transmission.
MeSH term(s)	Adult ; Child ; Humans ; Adolescent ; Aged ; Incidence ; SARS-CoV-2 ; Texas/epidemiology ; COVID-19/epidemiology ; COVID-19/prevention & control ; Disease Outbreaks ; Vaccination
Language	English
Publishing date	2023-02-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2668791-4
ISSN	2048-7207 ; 2048-7193
ISSN (online)	2048-7207
ISSN	2048-7193
DOI	10.1093/jpids/piac086
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