Evaluation of the IP-10 mRNA release assay for diagnosis of TB in HIV-infected individuals

HIV-infected individuals are susceptible to Mycobacterium tuberculosis (M.tb) infection and are at high risk of developing active tuberculosis (TB). Interferon-gamma release assays (IGRAs) are auxiliary tools in the diagnosis of TB. However, the performance of IGRAs in HIV-infected individuals is suboptimal, which limits clinical application. Interferon-inducible protein 10 (IP-10) is an alternative biomarker for identifying M.tb infection due to its high expression after stimulation with M.tb antigens. However, whether IP-10 mRNA constitutes a target for the diagnosis of TB in HIV-infected individuals is unknown. Thus, we prospectively enrolled HIV-infected patients with suspected active TB from five hospitals between May 2021 and May 2022, and performed the IGRA test (QFT-GIT) alongside the IP-10 mRNA release assay on peripheral blood. Of the 216 participants, 152 TB patients and 48 non-TB patients with a conclusive diagnosis were included in the final analysis. The number of indeterminate results of IP-10 mRNA release assay (13/200, 6.5%) was significantly lower than that of the QFT-GIT test (42/200, 21.0%) (P = 0.000026). IP-10 mRNA release assay had a sensitivity of 65.3% (95%CI 55.9% – 73.8%) and a specificity of 74.2% (95%CI 55.4% – 88.1%), respectively; while the QFT-GIT test had a sensitivity of 43.2% (95%CI 34.1% – 52.7%) and a specificity of 87.1% (95%CI 70.2% – 96.4%), respectively. The sensitivity of the IP-10 mRNA release assay was significantly higher than that of QFT-GIT test (P = 0.00062), while no significant difference was detected between the specificities of these two tests (P = 0.198). The IP-10 mRNA release assay showed a lower dependence on CD4+ T cells than that of QFT-GIT test. This was evidenced by the fact that the QFT-GIT test had a higher number of indeterminate results and a lower sensitivity when the CD4+ T cells counts were decreased (P < 0.05), while no significant difference in the number of indeterminate results and sensitivity were observed for the IP-10 mRNA release assay among HIV-infected individuals with varied CD4+T cells counts (P > 0.05). Therefore, our study suggested that M.tb specific IP-10 mRNA is a better biomarker for diagnosis of TB in HIV-infected individuals

Characterization and Expression of Glutamate Dehydrogenase in Response to Acute Salinity Stress in the Chinese Mitten Crab, Eriocheir sinensis

Glutamate dehydrogenase (GDH) is a key enzyme for the synthesis and catabolism of glutamic acid, proline and alanine, which are important osmolytes in aquatic animals. However, the response of GDH gene expression to salinity alterations has not yet been determined in macro-crustacean species.GDH cDNA was isolated from Eriocheir sinensis. Then, GDH gene expression was analyzed in different tissues from normal crabs and the muscle of crabs following transfer from freshwater (control) directly to water with salinities of 16‰ and 30‰, respectively. Full-length GDH cDNA is 2,349 bp, consisting of a 76 bp 5'- untranslated region, a 1,695 bp open reading frame encoding 564 amino acids and a 578 bp 3'- untranslated region. E. sinensis GDH showed 64-90% identity with protein sequences of mammalian and crustacean species. Muscle was the dominant expression source among all tissues tested. Compared with the control, GDH expression significantly increased at 6 h in crabs transferred to 16‰ and 30‰ salinity, and GDH expression peaked at 48 h and 12 h, respectively, with levels approximately 7.9 and 8.5 fold higher than the control. The free amino acid (FAA) changes in muscle, under acute salinity stress (16‰ and 30‰ salinities), correlated with GDH expression levels. Total FAA content in the muscle, which was based on specific changes in arginine, proline, glycine, alanine, taurine, serine and glutamic acid, tended to increase in crabs following transfer to salt water. Among these, arginine, proline and alanine increased significantly during salinity acclimation and accounted for the highest proportion of total FAA.E. sinensis GDH is a conserved protein that serves important functions in controlling osmoregulation. We observed that higher GDH expression after ambient salinity increase led to higher FAA metabolism, especially the synthesis of glutamic acid, which increased the synthesis of proline and alanine to meet the demand of osmoregulation at hyperosmotic conditions

The Earth BioGenome Project 2020: Starting the clock

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The Earth BioGenome Project 2020: Starting the clock.

© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lewin, H. A., Richards, S., Lieberman Aiden, E., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, Mark L., Cai, J., Caperello, N. D., Carlson, K., Castilla-Rubio, J. C., Chaw, S-M., Chen, L., Childers, A. K., Coddington, J. A., Conde, D. A., Corominas, M., Crandall, K. A., Crawford, A. J., DiPalma, F., Durbin, R., Ebenezer, T. E., Edwards, S. V., Fedrigo, O., Flicek, P., Formenti, G., Gibbs, R. A., Gilbert, M. Thomas P., Goldstein, M. M., Graves, J. M., Greely, H. T., Grigoriev, I. V., Hackett, K. J., Hall, N., Haussler, D., Helgen, K. M., Hogg, C. J., Isobe, S., Jakobsen, K. S., Janke, A., Jarvis, E. D., Johnson, W. E., Jones, S. J. M., Karlsson, E. K., Kersey, P. J., Kim, J-H., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Leebens-Mack, J. H., Li, X., Lindblad-Toh, K., Liu, X., Lopez, J. V., Marques-Bonet, T., Mazard, S., Mazet, J. A. K., Mazzoni, C. J., Myers, E. W., O’Neill, R. J., Paez, S., Park, H., Robinson, G. E., Roquet, C., Ryder, O. A., Sabir, J. S. M., Shaffer, H. B., Shank, T. M., Sherkow, J. S., Soltis, P. S., Tang, B., Tedersoo, L., Uliano-Silva, M., Wang, K., Wei, X., Wetzer, R., Wilson, J. L., Xu, X., Yang, H., Yoder, A. D., Zhang, G. The Earth BioGenome Project 2020: starting the clock. Proceedings of the National Academy of Sciences of the United States of America, 119(4), (2022): e2115635118, https://doi.org/10.1073/pnas.2115635118.November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phase has ended and the clock has started on reaching the EBP’s major milestones. This Special Feature explores the many facets of the EBP, including a review of progress, a description of major scientific goals, exemplar projects, ethical legal and social issues, and applications of biodiversity genomics. In this Introduction, we summarize the current status of the EBP, held virtually October 5 to 9, 2020, including recent updates through February 2021. References to the nine Perspective articles included in this Special Feature are cited to guide the reader toward deeper understanding of the goals and challenges facing the EBP

Hypogastrura sheyangensis Jiang, Tang & Chen, 2007, sp. nov.

<i>Hypogastrura sheyangensis</i> sp. nov. <p>Figs 1–21, Tab. 1</p> <p> <b>Type material.</b> Holotype, female, China: Jiangsu Province, Yancheng, Sheyang County, National Nature Reserve of Red-Crowned Cranes, 26.iv.2006, collection number C9465, coll. Ji-Qiang Qu <i>et al</i>. Paratypes: 7 females and 9 males, 12 in alcohol, same data as holotype. Deposited in the Department of Biology, Nanjing University, China.</p> <p> <b>Description.</b></p> <p>Size. Maximum body length: up to 1.5 mm.</p> <p>Colour. Dorsum of body, antennae and legs violet-black, ventral side paler. Eye patches dark.</p> <p>Vestiture. Tegumentary granulation: coarse, dorsal of Abd. V with 5–7 (usually 6) granules between p1 setae.</p> <p> Antennae. Antennae short, 0.55–0.75 and 0.09–0.16 times as long as cephalic diagonal and body length respectively. Ratio of length of antennal segments as I: II: III: IV = 1: 0.7–1.3: 1.0–1.4: 1.4–1.8. Ant. IV with simple apical bulb; dorsally with 10 differentiated sensilla, subapical vesicle (os) and microsensillum (ms); ventrally with 3 short and pointed setae inserted in papillae (Figs 10 and 11). Ant. III organ with 2 small rod-like sensilla in separate foveae and two guard sensilla. Ventral microsensillum also present on Ant. III. Ant. II with 13 setae. Ant. I with 8 setae including <i>p</i> seta (Fig. 10).</p> <p>Head. Tubercles and spines absent. Eyes 8+8; eye patch with three setae, Oc2 longer than Oc1 and Oc3 (Fig. 8). Postantennal organ 1.2–2.5 times as large as nearest eye in diameter, composed of 4 lobes, without accessory tubercle (Fig. 8).Labral setal formula 4/5, 5, 4, lateral setae of anterior row slightly thickened with tip bent inwards, labral margin without papillae (Fig. 5). Ventral cephalic chaetotaxy (after Fjellberg 1998 /99) with 6 setae in px, 4 in bm, 5 in bl, and 3 in plb (Fig. 2). Labial palp with 5 papillae (A–E) (after Fjellberg 1998 /99), guard setae a1, d1, e7 and lateral process absent (Fig. 20). Maxilla with 6 lamellae, lamella 1 with long filaments, lamellae 1 and 2 longer than maxillary teeth, lamella 6 obviously longer than lamellae 3 and 5 (Fig. 12). Maxillary outer lobe with 2 sublobal hairs (Fig. 3). Dorsal cephalic chaetotaxy (after Yosii 1960) shown in Fig. 4. Differentiation between microsetae and macrosetae indistinct. Dorsal setae on thoracic and abdominal segments generally arranged in one row (p row), two (a and p rows) or three rows (a, m and p rows). All setae divided into three types: 1) macrosetae on Abd. V–VI (Fig. 6 c, A1, A2… and P1, P2…); 2) microsetae (Fig. 6 b, a1, a2…, m1, m2… and p1, p2…); 3) long, smooth and curved sensilla (Fig. 6 a: s).</p> <p>Thorax. Dorsal chaetotaxy shown in Fig. 1. Th. I with 3+3 setae in p row, usually p5 longer than p1 and p4. Th. II with 3 rows of setae, 6+6 setae in a row, as a1-6; usually 4+4 setae in m row, as m1, m4-5 and m7, occasionally m6 present, m2 and m3 absent, m7 as s; 6+6 setae in p row, as p1–6, p4 as s. Th. III with 3 rows of setae, 6+6 setae in a row, as a1-2 and a4–7; 4+4 setae in m row, as m1, m4-5 and m7, m2 and m3 absent, m7 as s; 6+6 setae in p row, as p1–6, p4 as s. No seta on thoracic sterna II–III. Legs with unguis well-developed, with one inner tooth at 3/5 distance of its inner edge from base. Unguiculus lance-shaped, with tip of apical filament reaching 1/2 distance of inner edge of unguis. Tibiotarsus with one weakly knobbed tenent hair (Fig. 13). Hind leg with 3 setae on subcoxa, 7 (rarely 8) setae on coxa, 7 setae on trochanter, 12 setae on femur, 18 setae on tibiotarsus including tenent hair (Fig. 19).</p> <p>Abdomen. Dorsal chaetotaxy showed in Fig. 9. Abd. I with three rows of setae, 5+5 setae in a row, as a1-2 and a4-6; 3+3 setae in m row, as m3-4 and m7; 7+7 setae in p row, as p1–7, p5 as s. Abd. II with three rows of setae, 6+6 setae in a row, as a1-2 and a4-7; 3+3 setae in m row, as m3-4 and m7; 7+7 setae in p row, as p1–7, p5 as s. Abd. III with three rows of setae, 7+7 setae in a row, as a1–7; 3+3 setae in m row, as m3-4 and m7; 7+7 setae in p row, as p1–7, p5 as s. Abd. IV with three rows of setae, 5+5 setae in a row, as a1–5; 4+4 setae in m row, as m1 and m3– 5; 5+5 setae in p row, as p1–5, p4 as s, length ratio of p4 (s): p5 = 1.9–2.3: 1. Abd. V with two rows of setae, 5+5 setae in a row, as A1–5; 5+5 setae in p row, as P1–5, P3 as seta s. Abd. VI with 2 rows of setae, 3+3 setae in a row, Note: * the same seta respectively in figs. 10 & 11.</p> <p>as A1-3; 2+2 setae in p row (Fig. 18). Ventral tube short, with 4+4 setae (Fig. 17). Tenaculum with 4 teeth on each ramus, no seta on corpus (Fig. 7). Manubrium (posterior) usually with 14 (rarely 13 or 15) setae on each side. Dens posteriorly with coarse granules (Fig. 21) and 7 setae, ratio of length of subbasal seta to basal seta as 2.0–2.7:1. Mucro with apex slightly curved, outer lamella long and slender, without inner lamella (Fig. 14). Length ratio of dens to mucro = 1.8–2.5 (mean 2.2):1.</p> <p>Two short, straight anal spines on Abd. VI, slightly longer than their basal papillae (Fig. 18). Male and female genital plates respectively with 20–34 and 16–22 setae (Figs. 15 and 16).</p> <p> <b>Ecology.</b> In soil under the salt–tolerant plant, <i>Suaeda salsa</i> (L.), in the salt marsh at intertidal zone.</p> <p> <b>Etymology.</b> The new species is named after the type locality of Sheyang County.</p> <p> <b>Remarks.</b> The new species is characterised by p4 seta on Abd. IV as sensillum (p4 = s), which can distinguish it from all known species in the <i>manubrialis</i> group of the genus <i>Hypogastrura</i> except <i>H. matura</i> (Folsom) (<i>sensu</i> Christiansen & Bellinger, 1998). However, the new species has 10 dorsal sensilla on Ant. IV and coarse granules on dens whereas <i>H. matura</i> possess 8 sensilla on Ant. IV and fine granules on dens. The North American species <i>H. utahensis</i> (Wray) (<i>sensu</i> Christiansen & Bellinger, 1998) may be another species with the character (p4 = s) similar to the new species; however, it differs from the new species in the presence of trilobed postantennal organ, one or two setae in m row on Abd. V, 6–8 weakly differentiated sensilla on Ant. IV, the absence of <i>p</i> seta on Ant. I.</p> <p> The new species is similar to <i>H. manubrialis</i> (Tullberg) (<i>sensu</i> Babenko <i>et al</i>. 1994, Thibaud <i>et al</i>. 2004) in the following characters: 1) Th. II and Abd. IV without m2, Abd. V without m seta; 2) claw with a single inner tooth; 3) tibiotarsus with a single weakly knobbed tenent hair; 4) dens with 7 setae. The new species is also close to <i>H. arctandria</i> Fjellberg, 1988 and <i>H. assimilis</i> (Krausbauer) (<i>sensu</i> Babenko <i>et al</i>. 1994, Thibaud <i>et al</i>. 2004). However, the new species could be easily distinguished from the above mentioned three species by the characters showed in Tab. 1.</p> <p> Among the five Chinese species described in the genus <i>Hypogastrura</i>, only <i>H. yosii</i> Stach, 1964 is the member of <i>H. manubrialis</i> group. However, it differs from the new species in the presence of 6 dorsal sensilla on Ant. IV, the absence of <i>p</i> seta on Ant. I and inner tooth on claw.</p> <p> <b>TABLE 1.</b> Differences between <i>H. sheyangensis</i> <b>sp. nov.</b> and the most similar three species in <i>H. manubrialis –</i> group.</p>Published as part of <i>Jiang, Jigang, Tang, Boping & Chen, Jian-Xiu, 2007, A new species of the genus Hypogastrura from coastal wetlands of East China (Collembola: Hypogastruridae), pp. 63-68 in Zootaxa 1630</i> on pages 64-67, DOI: <a href="http://zenodo.org/record/179400">10.5281/zenodo.179400</a&gt

Germplasm Authentication of Mantis Shrimps (<i>Oratosquilla oratoria</i>) in China Sea by SNP and AS-PCR Method

1471-1473In the study, germplasm authentication of mantis shrimp in China sea was analyzed by SNP and AS-PCR method. Twenty-six stably single nucleotide polymorphisms (SNPs) between Bohai sea and South China sea were revealed, and population-specific primer pairs (BH065/BH326, SC065/SC326) were established based on SNPs. And topological structure analysis separated the mantis shrimps into two distinct lineages with 100% statistical support, which reveals significant divergence has happened in China sea though weak differentiation in morphology. These results showed SNPs and AS-PCR might be the useful tools for germplasm authentication of mantis shrimp

Global Boundedness in a Logarithmic Keller–Segel System

In this paper, we propose a user-friendly integral inequality to study the coupled parabolic chemotaxis system with singular sensitivity under the Neumann boundary condition. Under a low diffusion rate, the classical solution of this system is uniformly bounded. Our proof replies on the construction of the energy functional containing ∫Ω|v|4v2 with v>0. It is noteworthy that the inequality used in the paper may be applied to study other chemotaxis systems